diff --git a/changelog.d/fixes/13680-13681-batches-sweep-cap-shared-file.md b/changelog.d/fixes/13680-13681-batches-sweep-cap-shared-file.md
new file mode 100644
index 00000000000..79fb1524e90
--- /dev/null
+++ b/changelog.d/fixes/13680-13681-batches-sweep-cap-shared-file.md
@@ -0,0 +1 @@
+- **fix(db):** `DELETE /v1/batches/delete-completed` now caps the work it does per request and reports `hasMore` so a caller can resume, and the sweep no longer deletes a file that another batch still references (#13680, #13681)
diff --git a/open-sse/services/batchProcessor.ts b/open-sse/services/batchProcessor.ts
index 7b242e4851b..832dd464416 100644
--- a/open-sse/services/batchProcessor.ts
+++ b/open-sse/services/batchProcessor.ts
@@ -7,6 +7,7 @@ import {
   getBatch,
   getPendingBatches,
   getTerminalBatches,
+  isFileReferencedByOtherBatch,
   listBatchItemCheckpoints,
   markBatchItemError,
   markBatchItemProcessing,
@@ -253,13 +254,32 @@ async function cleanupExpiredBatches(): Promise<void> {
           : null;
       const outputExpiresAt = getBatchOutputExpiresAt(batch);
 
-      if (batch.inputFileId && inputExpiresAt && now > inputExpiresAt) {
+      // #13681: skip the soft-delete when some OTHER batch still references
+      // the same file id (e.g. one input file reused across batches) — a
+      // terminal batch's own expiry must not null a file a sibling still
+      // needs.
+      if (
+        batch.inputFileId &&
+        inputExpiresAt &&
+        now > inputExpiresAt &&
+        !isFileReferencedByOtherBatch(batch.inputFileId, [batch.id])
+      ) {
         deleteFile(batch.inputFileId);
       }
-      if (batch.outputFileId && outputExpiresAt && now > outputExpiresAt) {
+      if (
+        batch.outputFileId &&
+        outputExpiresAt &&
+        now > outputExpiresAt &&
+        !isFileReferencedByOtherBatch(batch.outputFileId, [batch.id])
+      ) {
         deleteFile(batch.outputFileId);
       }
-      if (batch.errorFileId && outputExpiresAt && now > outputExpiresAt) {
+      if (
+        batch.errorFileId &&
+        outputExpiresAt &&
+        now > outputExpiresAt &&
+        !isFileReferencedByOtherBatch(batch.errorFileId, [batch.id])
+      ) {
         deleteFile(batch.errorFileId);
       }
     }
diff --git a/src/app/api/v1/batches/delete-completed/route.ts b/src/app/api/v1/batches/delete-completed/route.ts
index 5e095fc845b..4cbb21d530b 100644
--- a/src/app/api/v1/batches/delete-completed/route.ts
+++ b/src/app/api/v1/batches/delete-completed/route.ts
@@ -95,6 +95,7 @@ export async function DELETE(request: Request) {
     apiKeyId: scope.apiKeyId,
     deletedBatches: result.deletedBatches,
     deletedFiles: result.deletedFiles,
+    hasMore: result.hasMore,
   };
   // A bulk delete is an audit event, not routine chatter: an instance-wide sweep
   // and any key-scoped sweep that actually removed rows log at warn so the trail
@@ -109,7 +110,12 @@ export async function DELETE(request: Request) {
   }
 
   return NextResponse.json(
-    { deleted: true, deletedBatches: result.deletedBatches, deletedFiles: result.deletedFiles },
+    {
+      deleted: true,
+      deletedBatches: result.deletedBatches,
+      deletedFiles: result.deletedFiles,
+      hasMore: result.hasMore,
+    },
     { headers: CORS_HEADERS }
   );
 }
diff --git a/src/lib/db/batches.ts b/src/lib/db/batches.ts
index 5282313ac21..4f98e58006d 100644
--- a/src/lib/db/batches.ts
+++ b/src/lib/db/batches.ts
@@ -387,22 +387,25 @@ export function deleteBatch(id: string): boolean {
 
   db.prepare("DELETE FROM batch_item_checkpoints WHERE batch_id = ?").run(id);
 
-  // Soft-delete associated files (input, output, error)
-  if (batch.inputFileId) {
+  // Soft-delete associated files (input, output, error) — but only when no
+  // OTHER batch still references the same file id (#13681). A file shared
+  // across batches (e.g. one input file reused for several batch submissions)
+  // must survive as long as any sibling batch still points at it.
+  if (batch.inputFileId && !isFileReferencedByOtherBatch(batch.inputFileId, [id])) {
     try {
       deleteFile(batch.inputFileId);
     } catch {
       /* ignore */
     }
   }
-  if (batch.outputFileId) {
+  if (batch.outputFileId && !isFileReferencedByOtherBatch(batch.outputFileId, [id])) {
     try {
       deleteFile(batch.outputFileId);
     } catch {
       /* ignore */
     }
   }
-  if (batch.errorFileId) {
+  if (batch.errorFileId && !isFileReferencedByOtherBatch(batch.errorFileId, [id])) {
     try {
       deleteFile(batch.errorFileId);
     } catch {
@@ -424,6 +427,47 @@ export type DeleteCompletedBatchesScope = { apiKeyId: string } | { allTenants: t
 /** Both sweep modes commit in chunks of this many batches (SEC-D, LEDGER-4). */
 export const INSTANCE_SWEEP_CHUNK = 200;
 
+/**
+ * Upper bound on the number of `INSTANCE_SWEEP_CHUNK`-sized chunks a single
+ * `deleteCompletedBatches` call may run (#13680). `sweepLoop` is a synchronous
+ * `for (;;)` over `better-sqlite3` — with no cap, one request could hold the
+ * Node.js event loop for as long as it takes to sweep every completed batch on
+ * the instance. 25 × 200 = 5000 batches/request is a judgment call, not a hard
+ * constraint; any caller with more to sweep gets `hasMore: true` back and
+ * resumes by calling again — resumption falls out naturally from rowid
+ * ordering plus delete-as-you-go (already-swept rows are gone, so the next
+ * SELECT picks up the next-lowest surviving rowid on its own; no cursor field
+ * needed).
+ */
+export const MAX_CHUNKS_PER_REQUEST = 25;
+
+/**
+ * True when some batch OTHER than one of `excludeBatchIds` still references
+ * `fileId` as its input/output/error file (#13681). Used before soft-deleting
+ * a file to avoid nulling content a surviving batch still needs. Binds
+ * `fileId` three times; when `excludeBatchIds` is empty the `NOT IN (...)`
+ * clause is dropped entirely rather than emitted empty (`NOT IN ()` is invalid
+ * SQL, and getting the guard wrong there would silently match everything).
+ */
+export function isFileReferencedByOtherBatch(fileId: string, excludeBatchIds: string[]): boolean {
+  const db = getDbInstance();
+  if (excludeBatchIds.length === 0) {
+    const row = db
+      .prepare(
+        "SELECT 1 FROM batches WHERE input_file_id = ? OR output_file_id = ? OR error_file_id = ? LIMIT 1"
+      )
+      .get(fileId, fileId, fileId);
+    return !!row;
+  }
+  const marks = excludeBatchIds.map(() => "?").join(",");
+  const row = db
+    .prepare(
+      `SELECT 1 FROM batches WHERE (input_file_id = ? OR output_file_id = ? OR error_file_id = ?) AND id NOT IN (${marks}) LIMIT 1`
+    )
+    .get(fileId, fileId, fileId, ...excludeBatchIds);
+  return !!row;
+}
+
 /**
  * Delete completed batches and the files they reference.
  *
@@ -457,10 +501,25 @@ export const INSTANCE_SWEEP_CHUNK = 200;
  * so the lowest-privilege caller — any valid API key — cannot hold the
  * instance's single writer for the length of its whole sweep. Each chunk stays
  * atomic: a failure inside chunk N leaves chunks < N committed, chunk N fully
- * rolled back, and rethrows. Inherent to per-chunk commits, in either mode: a
- * file shared by batches in two different chunks can be nulled by chunk 1
- * before chunk 2 fails; the surviving batch row is swept by the next run. The
- * returned totals sum the chunks.
+ * rolled back, and rethrows. Each chunk's file soft-deletes now check whether
+ * some batch OUTSIDE that chunk still references the file
+ * (`isFileReferencedByOtherBatch`, #13681) — a file shared with a
+ * non-completed sibling batch, or with a completed batch a LATER chunk hasn't
+ * reached yet, survives this chunk. The only case that check cannot see is
+ * pure timing: chunk 1 commits and nulls a file, then — before chunk 2 runs —
+ * a NEW batch is created reusing that same file id. That race is inherent to
+ * per-chunk commits and stays a known, accepted edge case; everything else
+ * (a concurrently existing sibling, in any status, in any chunk) is now
+ * guarded. The returned totals sum the chunks.
+ *
+ * A single call commits at most `MAX_CHUNKS_PER_REQUEST` chunks (#13680):
+ * `better-sqlite3` is synchronous, so an unbounded loop would hold the event
+ * loop for as long as it takes to sweep the whole key's/instance's backlog.
+ * When the cap is hit with more rows still pending, the call returns
+ * `hasMore: true` instead of continuing; the caller (the DELETE route) simply
+ * calls again. Resumption needs no cursor: swept rows are gone, `rowid` only
+ * increases, so the next call's `ORDER BY rowid LIMIT ?` picks up exactly
+ * where the previous call left off.
  *
  * The loop must make progress: it remembers the first id of the previous chunk
  * and throws if the next chunk starts with the same id — the DELETE removed
@@ -476,6 +535,7 @@ export const INSTANCE_SWEEP_CHUNK = 200;
 export function deleteCompletedBatches(scope: DeleteCompletedBatchesScope): {
   deletedBatches: number;
   deletedFiles: number;
+  hasMore: boolean;
 } {
   const scopeObj = scope && typeof scope === "object" ? scope : {};
   const allTenants = "allTenants" in scopeObj && scopeObj.allTenants === true;
@@ -517,6 +577,11 @@ export function deleteCompletedBatches(scope: DeleteCompletedBatchesScope): {
 
     let deletedFiles = 0;
     for (const fid of fileIds) {
+      // #13681: a file referenced by a batch outside this chunk (a different
+      // chunk not yet processed, or any non-completed batch — completed
+      // batches outside `ids` cannot exist since the SELECT above IS the
+      // chunk) must survive this chunk's sweep.
+      if (isFileReferencedByOtherBatch(fid, ids)) continue;
       try {
         // Key mode: only the key's OWN files. A batch may reference a file
         // another tenant (or nobody) owns; a bulk destructive sweep must not
@@ -541,11 +606,20 @@ export function deleteCompletedBatches(scope: DeleteCompletedBatchesScope): {
   // modes is the SELECT that produces the next chunk. No outer transaction —
   // the write lock is released between chunks (LEDGER-4/20/21).
   const sweepLoop = (nextIds: () => string[]) => {
-    const totals = { deletedBatches: 0, deletedFiles: 0 };
+    const totals = { deletedBatches: 0, deletedFiles: 0, hasMore: false };
     let previousFirstId: string | null = null;
+    let chunkCount = 0;
     for (;;) {
       const ids = nextIds();
       if (ids.length === 0) break;
+      // Chunk cap (#13680): a single request commits at most
+      // MAX_CHUNKS_PER_REQUEST chunks. This peek doesn't delete or count
+      // anything — it only tells the caller whether more work remains so it
+      // can call again (resumption is natural: already-swept rows are gone).
+      if (chunkCount >= MAX_CHUNKS_PER_REQUEST) {
+        totals.hasMore = true;
+        break;
+      }
       // Forward-progress guard (LEDGER-22): the chunk is re-selected from the
       // table after each commit, so a repeated first id means the previous
       // DELETE removed nothing and the loop would spin forever. A concurrent
@@ -557,6 +631,7 @@ export function deleteCompletedBatches(scope: DeleteCompletedBatchesScope): {
       const part = sweepIds(ids);
       totals.deletedBatches += part.deletedBatches;
       totals.deletedFiles += part.deletedFiles;
+      chunkCount++;
     }
     return totals;
   };
diff --git a/tests/unit/batches-delete-completed-route-scope.test.ts b/tests/unit/batches-delete-completed-route-scope.test.ts
index 76233cac5c4..9f0a6b4ff64 100644
--- a/tests/unit/batches-delete-completed-route-scope.test.ts
+++ b/tests/unit/batches-delete-completed-route-scope.test.ts
@@ -93,6 +93,7 @@ async function callDelete(headers: Record<string, string>, url: string = ROUTE_U
     deleted?: boolean;
     deletedBatches?: number;
     deletedFiles?: number;
+    hasMore?: boolean;
     error?: { message: string; type?: string; code?: string };
   };
   return { res, body };
@@ -115,6 +116,11 @@ describe("DELETE /api/v1/batches/delete-completed — caller scope (GHSA-wvxc-jp
     assert.strictEqual(body.deleted, true);
     assert.strictEqual(body.deletedBatches, 0, "key A owns no completed batch — nothing to sweep");
     assert.strictEqual(body.deletedFiles, 0);
+    assert.strictEqual(
+      body.hasMore,
+      false,
+      "the response must surface deleteCompletedBatches' hasMore continuation flag (#13680)"
+    );
     assert.ok(getBatch(victim.batch.id), "key B's completed batch must survive key A's sweep");
     assert.strictEqual(
       getFileContent(victim.file.id)?.toString(),
diff --git a/tests/unit/issue-13680-batches-delete-completed-unbounded-work.test.ts b/tests/unit/issue-13680-batches-delete-completed-unbounded-work.test.ts
new file mode 100644
index 00000000000..654dd01b349
--- /dev/null
+++ b/tests/unit/issue-13680-batches-delete-completed-unbounded-work.test.ts
@@ -0,0 +1,111 @@
+/**
+ * #13680 — DELETE /v1/batches/delete-completed does unbounded work per request.
+ *
+ * `deleteCompletedBatches` commits in chunks of `INSTANCE_SWEEP_CHUNK` (200), but
+ * the outer `sweepLoop` is a plain synchronous `for (;;)` that only stops when the
+ * table has no completed batch left — there is no cap on how many chunks a single
+ * request may run. better-sqlite3 is synchronous, so one request can hold the
+ * Node.js event loop for as long as it takes to sweep the ENTIRE table, and the
+ * caller has no way to ask for a bounded amount of work per call (no `hasMore`).
+ *
+ * This test seeds one row past the issue's own proposed cap
+ * (`MAX_CHUNKS_PER_REQUEST = 25` × `INSTANCE_SWEEP_CHUNK` = 5000) and asserts a
+ * single call stays within that bound and reports a continuation flag.
+ */
+import { describe, it, after } from "node:test";
+import assert from "node:assert";
+import fs from "node:fs";
+import os from "node:os";
+import path from "node:path";
+
+const TEST_DATA_DIR = fs.mkdtempSync(path.join(os.tmpdir(), "issue13680-"));
+process.env.DATA_DIR = TEST_DATA_DIR;
+
+const { createFile } = await import("../../src/lib/db/files.ts");
+const { createBatch, deleteCompletedBatches, INSTANCE_SWEEP_CHUNK, MAX_CHUNKS_PER_REQUEST } =
+  await import("../../src/lib/db/batches.ts");
+const { resetDbInstance } = await import("../../src/lib/db/core.ts");
+
+function seedCompletedBatch(label: string, apiKeyId: string | null = null) {
+  const file = createFile({
+    bytes: 1,
+    filename: `${label}.jsonl`,
+    purpose: "batch",
+    content: Buffer.from("x"),
+    apiKeyId,
+  });
+  return createBatch({
+    endpoint: "/v1/chat/completions",
+    completionWindow: "24h",
+    inputFileId: file.id,
+    status: "completed",
+    apiKeyId,
+  });
+}
+
+describe("#13680 — deleteCompletedBatches has a per-request chunk cap", () => {
+  after(() => {
+    resetDbInstance();
+    fs.rmSync(TEST_DATA_DIR, { recursive: true, force: true, maxRetries: 5, retryDelay: 100 });
+  });
+
+  it("stops after MAX_CHUNKS_PER_REQUEST chunks and reports hasMore instead of sweeping the whole table in one synchronous call", () => {
+    const cap = MAX_CHUNKS_PER_REQUEST * INSTANCE_SWEEP_CHUNK;
+    const total = cap + 1; // one row past the cap: proves the loop stops at it
+
+    for (let i = 0; i < total; i++) seedCompletedBatch(`issue13680-${i}`);
+
+    const result = deleteCompletedBatches({ allTenants: true }) as {
+      deletedBatches: number;
+      deletedFiles: number;
+      hasMore?: boolean;
+    };
+
+    assert.ok(
+      result.deletedBatches <= cap,
+      `expected a single request to sweep at most ${cap} batches (MAX_CHUNKS_PER_REQUEST=${MAX_CHUNKS_PER_REQUEST} × INSTANCE_SWEEP_CHUNK=${INSTANCE_SWEEP_CHUNK}), ` +
+        `but one call deleted ${result.deletedBatches} of ${total} in one synchronous pass — no per-request cap exists`
+    );
+    assert.strictEqual(
+      result.hasMore,
+      true,
+      "the result carries no continuation signal (`hasMore`), so a caller cannot tell more completed batches remain to sweep"
+    );
+  });
+
+  it("resumes across repeated calls until hasMore is false, sweeping the entire backlog", () => {
+    // Key-scoped on purpose: isolates this test's count from the leftover
+    // unowned batch the previous test's `allTenants` sweep may not have caught
+    // (its cap+1 seed leaves exactly one row past MAX_CHUNKS_PER_REQUEST), so
+    // the expected call count here stays exact regardless of test order.
+    const apiKeyId = "resume-key-13680";
+    const cap = MAX_CHUNKS_PER_REQUEST * INSTANCE_SWEEP_CHUNK;
+    const total = cap + 50;
+    for (let i = 0; i < total; i++) seedCompletedBatch(`issue13680-resume-${i}`, apiKeyId);
+
+    let totalDeleted = 0;
+    let hasMore = true;
+    let calls = 0;
+    while (hasMore) {
+      calls++;
+      if (calls > 10) throw new Error("resumption did not converge within 10 calls");
+      const result = deleteCompletedBatches({ apiKeyId }) as {
+        deletedBatches: number;
+        hasMore: boolean;
+      };
+      totalDeleted += result.deletedBatches;
+      hasMore = result.hasMore;
+    }
+
+    assert.strictEqual(
+      calls,
+      2,
+      "50 extra rows past one cap should resume in exactly one more call"
+    );
+    assert.strictEqual(
+      totalDeleted,
+      total,
+      "every seeded batch must be swept across the resumed calls"
+    );
+  });
+});
diff --git a/tests/unit/issue-13681-shared-file-across-batches.test.ts b/tests/unit/issue-13681-shared-file-across-batches.test.ts
new file mode 100644
index 00000000000..6fb85a3e398
--- /dev/null
+++ b/tests/unit/issue-13681-shared-file-across-batches.test.ts
@@ -0,0 +1,143 @@
+/**
+ * Repro for #13681 — the completed-batch sweep (deleteCompletedBatches /
+ * deleteBatch / cleanupExpiredBatches) nulls a file's content whenever ANY
+ * completed batch it deletes references that file id, without checking
+ * whether another batch — in progress, queued, or completed but outside the
+ * current sweep unit — still references the same file. A tenant that reuses
+ * one input file across two batches loses that file for the surviving batch.
+ *
+ * Self-isolating: DATA_DIR points at a fresh temp dir before any `@/lib/db/*`
+ * module loads.
+ */
+import { describe, it, after } from "node:test";
+import assert from "node:assert";
+import fs from "node:fs";
+import os from "node:os";
+import path from "node:path";
+
+const TEST_DATA_DIR = fs.mkdtempSync(path.join(os.tmpdir(), "issue-13681-"));
+process.env.DATA_DIR = TEST_DATA_DIR;
+
+const { createFile, getFile, getFileContent } = await import("../../src/lib/db/files.ts");
+const { createBatch, getBatch, deleteCompletedBatches, deleteBatch } =
+  await import("../../src/lib/db/batches.ts");
+const { resetDbInstance } = await import("../../src/lib/db/core.ts");
+
+describe("#13681 — shared file reference survives a sibling batch's deletion", () => {
+  after(() => {
+    resetDbInstance();
+    fs.rmSync(TEST_DATA_DIR, { recursive: true, force: true, maxRetries: 5, retryDelay: 100 });
+  });
+
+  it("deleteCompletedBatches must NOT null a file still referenced by a surviving in_progress batch", () => {
+    const apiKeyId = "key_shared_13681";
+    const sharedFile = createFile({
+      bytes: 8,
+      filename: "shared-input.jsonl",
+      purpose: "batch",
+      content: Buffer.from("shared-content"),
+      apiKeyId,
+    });
+
+    // Batch A: completed, will be swept and deleted.
+    const batchA = createBatch({
+      endpoint: "/v1/chat/completions",
+      completionWindow: "24h",
+      inputFileId: sharedFile.id,
+      status: "completed",
+      apiKeyId,
+    });
+
+    // Batch B: still in progress, reuses the SAME input file id, and is never
+    // touched by this sweep call.
+    const batchB = createBatch({
+      endpoint: "/v1/chat/completions",
+      completionWindow: "24h",
+      inputFileId: sharedFile.id,
+      status: "in_progress",
+      apiKeyId,
+    });
+
+    const result = deleteCompletedBatches({ apiKeyId });
+
+    assert.strictEqual(getBatch(batchA.id), null, "the completed batch is swept as expected");
+    assert.ok(getBatch(batchB.id), "the in-progress batch must survive the sweep");
+    assert.strictEqual(result.deletedBatches, 1, "only the completed batch counted as deleted");
+
+    // Expected/correct behavior: batch B is alive and still points at
+    // sharedFile.id, so the sweep must NOT have soft-deleted that file just
+    // because batch A (also swept) referenced the same file id.
+    assert.ok(getFile(sharedFile.id), "the shared file must survive — batch B still references it");
+    assert.notStrictEqual(
+      getFileContent(sharedFile.id),
+      null,
+      "the shared file's content must survive — batch B still references it"
+    );
+  });
+
+  it("deleteBatch (single) must NOT null a file still referenced by a sibling batch", () => {
+    const apiKeyId = "key_shared_single_13681";
+    const sharedFile = createFile({
+      bytes: 8,
+      filename: "shared-input-2.jsonl",
+      purpose: "batch",
+      content: Buffer.from("shared-content-2"),
+      apiKeyId,
+    });
+
+    const batchA = createBatch({
+      endpoint: "/v1/chat/completions",
+      completionWindow: "24h",
+      inputFileId: sharedFile.id,
+      status: "completed",
+      apiKeyId,
+    });
+    const batchB = createBatch({
+      endpoint: "/v1/chat/completions",
+      completionWindow: "24h",
+      inputFileId: sharedFile.id,
+      status: "in_progress",
+      apiKeyId,
+    });
+
+    const deleted = deleteBatch(batchA.id);
+
+    assert.strictEqual(deleted, true, "deleteBatch reports success for batch A");
+    assert.ok(getBatch(batchB.id), "batch B is untouched by deleteBatch(batchA.id)");
+    assert.notStrictEqual(
+      getFileContent(sharedFile.id),
+      null,
+      "the shared file's content must survive — batch B still references it"
+    );
+  });
+
+  it("deleteCompletedBatches DOES delete the file once the LAST referencing batch is gone (no regression toward never-delete)", () => {
+    const apiKeyId = "key_last_ref_13681";
+    const file = createFile({
+      bytes: 8,
+      filename: "last-ref.jsonl",
+      purpose: "batch",
+      content: Buffer.from("last-ref-content"),
+      apiKeyId,
+    });
+
+    const onlyBatch = createBatch({
+      endpoint: "/v1/chat/completions",
+      completionWindow: "24h",
+      inputFileId: file.id,
+      status: "completed",
+      apiKeyId,
+    });
+
+    const result = deleteCompletedBatches({ apiKeyId });
+
+    assert.strictEqual(getBatch(onlyBatch.id), null);
+    assert.strictEqual(result.deletedBatches, 1);
+    assert.strictEqual(
+      result.deletedFiles,
+      1,
+      "the file had no other referencing batch, so it must be deleted"
+    );
+    assert.strictEqual(getFile(file.id), null, "the file is gone once nothing else references it");
+  });
+});