diff --git a/turbopack/crates/turbo-persistence-tools/src/main.rs b/turbopack/crates/turbo-persistence-tools/src/main.rs
index 3c9633bd4a69..8a026c99aae5 100644
--- a/turbopack/crates/turbo-persistence-tools/src/main.rs
+++ b/turbopack/crates/turbo-persistence-tools/src/main.rs
@@ -39,7 +39,7 @@ fn main() -> Result<()> {
         {
             println!(
                 "  SST {sequence_number:08}.sst: {min_hash:016x} - {max_hash:016x} (p = 1/{})",
-                u64::MAX / (max_hash - min_hash)
+                u64::MAX / (max_hash - min_hash + 1)
             );
             println!("    AQMF {aqmf_entries} entries = {} KiB", aqmf_size / 1024);
             println!(
diff --git a/turbopack/crates/turbo-persistence/src/db.rs b/turbopack/crates/turbo-persistence/src/db.rs
index 13d426b9971e..e1db68ae0959 100644
--- a/turbopack/crates/turbo-persistence/src/db.rs
+++ b/turbopack/crates/turbo-persistence/src/db.rs
@@ -525,7 +525,12 @@ impl TurboPersistence {
                         (seq, range.min_hash, range.max_hash, size)
                     })
                     .collect::<Vec<_>>();
-                (meta.sequence_number(), meta.family(), ssts)
+                (
+                    meta.sequence_number(),
+                    meta.family(),
+                    ssts,
+                    meta.obsolete_sst_files().to_vec(),
+                )
             })
             .collect::<Vec<_>>();
 
@@ -606,7 +611,7 @@ impl TurboPersistence {
             writeln!(log, "Time {time}")?;
             let span = time.until(Timestamp::now())?;
             writeln!(log, "Commit {seq:08} {keys_written} keys in {span:#}")?;
-            for (seq, family, ssts) in new_meta_info {
+            for (seq, family, ssts, obsolete) in new_meta_info {
                 writeln!(log, "{seq:08} META family:{family}",)?;
                 for (seq, min, max, size) in ssts {
                     writeln!(
@@ -615,6 +620,9 @@ impl TurboPersistence {
                         size / 1024 / 1024
                     )?;
                 }
+                for seq in obsolete {
+                    writeln!(log, "  {seq:08} OBSOLETE SST")?;
+                }
             }
             new_sst_files.sort_unstable_by_key(|(seq, _)| *seq);
             for (seq, _) in new_sst_files.iter() {
diff --git a/turbopack/crates/turbo-persistence/src/meta_file.rs b/turbopack/crates/turbo-persistence/src/meta_file.rs
index f48719b97351..9a2d8f7b874b 100644
--- a/turbopack/crates/turbo-persistence/src/meta_file.rs
+++ b/turbopack/crates/turbo-persistence/src/meta_file.rs
@@ -183,6 +183,8 @@ pub struct MetaFile {
     family: u32,
     /// The entries of the file.
     entries: Vec<MetaEntry>,
+    /// The entries that have been marked as obsolete.
+    obsolete_entries: Vec<u32>,
     /// The obsolete SST files.
     obsolete_sst_files: Vec<u32>,
     /// The memory mapped file.
@@ -247,6 +249,7 @@ impl MetaFile {
             sequence_number,
             family,
             entries,
+            obsolete_entries: Vec::new(),
             obsolete_sst_files,
             mmap,
         };
@@ -276,11 +279,21 @@ impl MetaFile {
 
     pub fn retain_entries(&mut self, mut predicate: impl FnMut(u32) -> bool) -> bool {
         let old_len = self.entries.len();
-        self.entries
-            .retain(|entry| predicate(entry.sst_data.sequence_number));
+        self.entries.retain(|entry| {
+            if predicate(entry.sst_data.sequence_number) {
+                true
+            } else {
+                self.obsolete_entries.push(entry.sst_data.sequence_number);
+                false
+            }
+        });
         old_len != self.entries.len()
     }
 
+    pub fn obsolete_entries(&self) -> &[u32] {
+        &self.obsolete_entries
+    }
+
     pub fn has_active_entries(&self) -> bool {
         !self.entries.is_empty()
     }
diff --git a/turbopack/crates/turbo-persistence/src/meta_file_builder.rs b/turbopack/crates/turbo-persistence/src/meta_file_builder.rs
index f0471976f697..eb78f03ff90b 100644
--- a/turbopack/crates/turbo-persistence/src/meta_file_builder.rs
+++ b/turbopack/crates/turbo-persistence/src/meta_file_builder.rs
@@ -35,17 +35,18 @@ impl MetaFileBuilder {
     }
 
     #[tracing::instrument(level = "trace", skip_all)]
-    pub fn write(&self, db_path: &Path, seq: u32) -> Result<File> {
+    pub fn write(self, db_path: &Path, seq: u32) -> Result<File> {
         let file = db_path.join(format!("{seq:08}.meta"));
         self.write_internal(&file)
             .with_context(|| format!("Unable to write meta file {seq:08}.meta"))
     }
 
-    fn write_internal(&self, file: &Path) -> io::Result<File> {
+    fn write_internal(mut self, file: &Path) -> io::Result<File> {
         let mut file = BufWriter::new(File::create(file)?);
         file.write_u32::<BE>(0xFE4ADA4A)?; // Magic number
         file.write_u32::<BE>(self.family)?;
 
+        self.obsolete_sst_files.sort();
         file.write_u32::<BE>(self.obsolete_sst_files.len() as u32)?;
         for obsolete_sst in &self.obsolete_sst_files {
             file.write_u32::<BE>(*obsolete_sst)?;
diff --git a/turbopack/crates/turbo-persistence/src/sst_filter.rs b/turbopack/crates/turbo-persistence/src/sst_filter.rs
index c0c6520dbaca..ca562880666d 100644
--- a/turbopack/crates/turbo-persistence/src/sst_filter.rs
+++ b/turbopack/crates/turbo-persistence/src/sst_filter.rs
@@ -19,6 +19,15 @@ impl SstFilter {
 
     /// Phase 1: Apply the filter to the meta file and update the state in the filter.
     pub fn apply_filter(&mut self, meta: &mut MetaFile) {
+        // Already obsolete entries need to be considered for usage computation
+        for seq in meta.obsolete_entries() {
+            if let Some(state) = self.0.get_mut(seq)
+                && matches!(state, SstState::UnusedObsolete)
+            {
+                // the obsolete state is used now
+                *state = SstState::Obsolete;
+            }
+        }
         meta.retain_entries(|seq| match self.0.entry(seq) {
             Entry::Occupied(mut e) => {
                 let state = e.get_mut();
diff --git a/turbopack/crates/turbo-persistence/src/tests.rs b/turbopack/crates/turbo-persistence/src/tests.rs
index f812eb6ea9f5..8e68e8a30310 100644
--- a/turbopack/crates/turbo-persistence/src/tests.rs
+++ b/turbopack/crates/turbo-persistence/src/tests.rs
@@ -1,4 +1,4 @@
-use std::time::Instant;
+use std::{fs, time::Instant};
 
 use anyhow::Result;
 use rayon::iter::{IntoParallelIterator, ParallelIterator};
@@ -557,3 +557,99 @@ fn partial_compaction() -> Result<()> {
 
     Ok(())
 }
+
+#[test]
+fn merge_file_removal() -> Result<()> {
+    let tempdir = tempfile::tempdir()?;
+    let path = tempdir.path();
+
+    let _ = fs::remove_dir_all(path);
+
+    const READ_COUNT: u32 = 2_000; // we'll read every 10th value, so writes are 10x this value
+    fn put(b: &WriteBatch<(u8, [u8; 4]), 1>, key: u8, value: u32) -> Result<()> {
+        for i in 0..(READ_COUNT * 10) {
+            b.put(
+                0,
+                (key, i.to_be_bytes()),
+                value.to_be_bytes().to_vec().into(),
+            )?;
+        }
+        Ok(())
+    }
+    fn check(db: &TurboPersistence, key: u8, value: u32) -> Result<()> {
+        for i in 0..READ_COUNT {
+            // read every 10th item
+            let i = i * 10;
+            assert_eq!(
+                db.get(0, &(key, i.to_be_bytes()))?.as_deref(),
+                Some(&value.to_be_bytes()[..]),
+                "Key {key} {i} expected {value}"
+            );
+        }
+        Ok(())
+    }
+    fn iter_bits(v: u32) -> impl Iterator<Item = u8> {
+        (0..32u8).filter(move |i| v & (1 << i) != 0)
+    }
+
+    {
+        println!("--- Init ---");
+        let db = TurboPersistence::open(path.to_path_buf())?;
+        let b = db.write_batch::<_, 1>()?;
+        for j in 0..=255 {
+            put(&b, j, 0)?;
+        }
+        db.commit_write_batch(b)?;
+        db.shutdown()?;
+    }
+
+    let mut expected_values = [0; 256];
+
+    for i in 1..50 {
+        println!("--- Iteration {i} ---");
+        let i = i * 37;
+        println!("Add more entries");
+        {
+            let db = TurboPersistence::open(path.to_path_buf())?;
+            let b = db.write_batch::<_, 1>()?;
+            for j in iter_bits(i) {
+                println!("Put {j} = {i}");
+                expected_values[j as usize] = i;
+                put(&b, j, i)?;
+            }
+            db.commit_write_batch(b)?;
+
+            for j in 0..32 {
+                check(&db, j, expected_values[j as usize])?;
+            }
+
+            db.shutdown()?;
+        }
+
+        println!("Compaction");
+        {
+            let db = TurboPersistence::open(path.to_path_buf())?;
+
+            db.compact(3.0, 3, u64::MAX)?;
+
+            for j in 0..32 {
+                check(&db, j, expected_values[j as usize])?;
+            }
+
+            db.shutdown()?;
+        }
+
+        println!("Restore check");
+        {
+            let db = TurboPersistence::open(path.to_path_buf())?;
+
+            for j in 0..32 {
+                check(&db, j, expected_values[j as usize])?;
+            }
+
+            db.shutdown()?;
+        }
+    }
+
+    Ok(())
+}