diff --git a/server/filestore.go b/server/filestore.go
index 62e23a63df9..5de4b91d712 100644
--- a/server/filestore.go
+++ b/server/filestore.go
@@ -4096,8 +4096,9 @@ func (mb *msgBlock) compact() {
 		if !isDeleted(seq) {
 			// Check for tombstones.
 			if seq&tbit != 0 {
-				// If we are last mb we should consider to keep these unless the tombstone reflects a seq in this mb.
-				if mb == mb.fs.lmb && seq < fseq {
+				seq = seq &^ tbit
+				// If this entry is for a lower seq than ours then keep around.
+				if seq < fseq {
 					nbuf = append(nbuf, buf[index:index+rl]...)
 				}
 			} else {
@@ -4153,6 +4154,9 @@ func (mb *msgBlock) compact() {
 		return
 	}
 
+	// Make sure to sync
+	mb.needSync = true
+
 	// Capture the updated rbytes.
 	mb.rbytes = uint64(len(nbuf))
 
@@ -6994,6 +6998,9 @@ func (fs *fileStore) Compact(seq uint64) (uint64, error) {
 		if smb != fs.lmb {
 			smb.dirtyCloseWithRemove(true)
 			deleted++
+		} else {
+			// Make sure to sync changes.
+			smb.needSync = true
 		}
 		// Update fs first here as well.
 		fs.state.FirstSeq = atomic.LoadUint64(&smb.last.seq) + 1
diff --git a/server/filestore_test.go b/server/filestore_test.go
index 564512f5756..68dd1f90a4c 100644
--- a/server/filestore_test.go
+++ b/server/filestore_test.go
@@ -6897,6 +6897,53 @@ func TestFileStoreFSSExpireNumPending(t *testing.T) {
 	fs.mu.RUnlock()
 }
 
+// We want to ensure that recovery of deleted messages survives no index.db and compactions.
+func TestFileStoreRecoverWithRemovesAndNoIndexDB(t *testing.T) {
+	sd := t.TempDir()
+	fs, err := newFileStore(
+		FileStoreConfig{StoreDir: sd, BlockSize: 250},
+		StreamConfig{Name: "zzz", Subjects: []string{"foo.*"}, Storage: FileStorage})
+	require_NoError(t, err)
+	defer fs.Stop()
+
+	msg := []byte("abc")
+	for i := 1; i <= 10; i++ {
+		fs.StoreMsg(fmt.Sprintf("foo.%d", i), nil, msg)
+	}
+	fs.RemoveMsg(1)
+	fs.RemoveMsg(2)
+	fs.RemoveMsg(8)
+
+	var ss StreamState
+	fs.FastState(&ss)
+	require_Equal(t, ss.FirstSeq, 3)
+	require_Equal(t, ss.LastSeq, 10)
+	require_Equal(t, ss.Msgs, 7)
+
+	// Compact last block.
+	fs.mu.RLock()
+	lmb := fs.lmb
+	fs.mu.RUnlock()
+	lmb.mu.Lock()
+	lmb.compact()
+	lmb.mu.Unlock()
+	// Stop but remove index.db
+	sfile := filepath.Join(sd, msgDir, streamStreamStateFile)
+	fs.Stop()
+	os.Remove(sfile)
+
+	fs, err = newFileStore(
+		FileStoreConfig{StoreDir: sd},
+		StreamConfig{Name: "zzz", Subjects: []string{"foo.*"}, Storage: FileStorage})
+	require_NoError(t, err)
+	defer fs.Stop()
+
+	fs.FastState(&ss)
+	require_Equal(t, ss.FirstSeq, 3)
+	require_Equal(t, ss.LastSeq, 10)
+	require_Equal(t, ss.Msgs, 7)
+}
+
 ///////////////////////////////////////////////////////////////////////////
 // Benchmarks
 ///////////////////////////////////////////////////////////////////////////