diff --git a/server/src/main/java/org/elasticsearch/index/engine/InternalEngine.java b/server/src/main/java/org/elasticsearch/index/engine/InternalEngine.java
index 1ed0f5d6f7994..0495290c29fd9 100644
--- a/server/src/main/java/org/elasticsearch/index/engine/InternalEngine.java
+++ b/server/src/main/java/org/elasticsearch/index/engine/InternalEngine.java
@@ -261,10 +261,14 @@ private static LocalCheckpointTracker createLocalCheckpointTracker(EngineConfig
             // Thus, we need to restore the LocalCheckpointTracker bit by bit to ensure the consistency between LocalCheckpointTracker and
             // Lucene index. This is not the only solution since we can bootstrap max_seq_no_of_updates with max_seq_no of the commit to
             // disable the MSU optimization during recovery. Here we prefer to maintain the consistency of LocalCheckpointTracker.
-            if (localCheckpoint < maxSeqNo && engineConfig.getIndexSettings().isSoftDeleteEnabled()) {
+            // The max_seq_no of Lucene commit in the old indices might be smaller than seq_no of some documents in the commit.
+            // We have to rebuild the LocalCheckpointTracker for those indices. See https://github.com/elastic/elasticsearch/pull/38879.
+            // Note that this bug affects only indices created between 6.5.0 and 6.6.1 with soft-deletes is explicitly enabled.
+            final boolean mustRebuild = engineConfig.getIndexSettings().getIndexVersionCreated().before(Version.V_6_6_2);
+            if (engineConfig.getIndexSettings().isSoftDeleteEnabled() && (localCheckpoint < maxSeqNo || mustRebuild)) {
                 try (Searcher searcher = searcherSupplier.get()) {
-                    Lucene.scanSeqNosInReader(searcher.getDirectoryReader(), localCheckpoint + 1, maxSeqNo,
-                        tracker::markSeqNoAsCompleted);
+                    final long toSeqNo = mustRebuild ? Long.MAX_VALUE : maxSeqNo;
+                    Lucene.scanSeqNosInReader(searcher.getDirectoryReader(), localCheckpoint + 1, toSeqNo, tracker::markSeqNoAsCompleted);
                 }
             }
             return tracker;
diff --git a/server/src/test/java/org/elasticsearch/index/engine/InternalEngineTests.java b/server/src/test/java/org/elasticsearch/index/engine/InternalEngineTests.java
index b5e34b7218417..e201e9fb78f89 100644
--- a/server/src/test/java/org/elasticsearch/index/engine/InternalEngineTests.java
+++ b/server/src/test/java/org/elasticsearch/index/engine/InternalEngineTests.java
@@ -132,6 +132,7 @@
 import org.elasticsearch.index.translog.TranslogConfig;
 import org.elasticsearch.indices.breaker.NoneCircuitBreakerService;
 import org.elasticsearch.test.IndexSettingsModule;
+import org.elasticsearch.test.VersionUtils;
 import org.hamcrest.MatcherAssert;
 import org.hamcrest.Matchers;
 
@@ -5632,6 +5633,61 @@ public void testRebuildLocalCheckpointTracker() throws Exception {
         }
     }
 
+    /**
+     * Simulate a bug in https://github.com/elastic/elasticsearch/pull/38879 where the max_seq_no
+     * of the index commit can be smaller than seq_no of some documents in the commit.
+     */
+    public void testAlwaysRebuildLocalCheckpointForOldIndex() throws Exception {
+        Settings.Builder settings = Settings.builder()
+            .put(defaultSettings.getSettings())
+            .put(IndexMetaData.SETTING_VERSION_CREATED, VersionUtils.randomVersionBetween(random(), Version.V_6_5_0, Version.V_6_6_1))
+            .put(IndexSettings.INDEX_SOFT_DELETES_SETTING.getKey(), true);
+        final IndexMetaData indexMetaData = IndexMetaData.builder(defaultSettings.getIndexMetaData()).settings(settings).build();
+        final IndexSettings indexSettings = IndexSettingsModule.newIndexSettings(indexMetaData);
+        Path translogPath = createTempDir();
+        List<Engine.Operation> operations = generateHistoryOnReplica(between(1, 500), randomBoolean(), randomBoolean(), randomBoolean());
+        final AtomicLong globalCheckpoint = new AtomicLong(SequenceNumbers.NO_OPS_PERFORMED);
+        try (Store store = createStore()) {
+            EngineConfig config = config(indexSettings, store, translogPath, NoMergePolicy.INSTANCE, null, null, globalCheckpoint::get);
+            final List<DocIdSeqNoAndTerm> docs;
+            try (InternalEngine engine = createEngine(config)) {
+                for (Engine.Operation op : operations) {
+                    applyOperation(engine, op);
+                    if (randomInt(100) < 10) {
+                        engine.flush();
+                        globalCheckpoint.set(randomLongBetween(globalCheckpoint.get(), engine.getLocalCheckpoint()));
+                    }
+                }
+                globalCheckpoint.set(randomLongBetween(globalCheckpoint.get(), engine.getLocalCheckpoint()));
+                engine.syncTranslog();
+                docs = getDocIds(engine, true);
+            }
+            trimUnsafeCommits(config);
+            // Simulate a bug in https://github.com/elastic/elasticsearch/pull/38879 where max_seq_no is smaller than seq_no of some docs.
+            if (randomBoolean()) {
+                IndexWriterConfig iwc = new IndexWriterConfig(null)
+                    .setSoftDeletesField(Lucene.SOFT_DELETES_FIELD)
+                    .setCommitOnClose(false)
+                    .setMergePolicy(NoMergePolicy.INSTANCE)
+                    .setOpenMode(IndexWriterConfig.OpenMode.APPEND);
+                try (IndexWriter writer = new IndexWriter(config.getStore().directory(), iwc)) {
+                    Map<String, String> userData = new HashMap<>();
+                    writer.getLiveCommitData().forEach(e -> userData.put(e.getKey(), e.getValue()));
+                    SequenceNumbers.CommitInfo commitInfo = SequenceNumbers.loadSeqNoInfoFromLuceneCommit(userData.entrySet());
+                    long maxSeqNo = randomLongBetween(commitInfo.localCheckpoint, commitInfo.maxSeqNo);
+                    userData.put(SequenceNumbers.MAX_SEQ_NO, Long.toString(maxSeqNo));
+                    writer.setLiveCommitData(userData.entrySet());
+                    writer.commit();
+                }
+            }
+            try (InternalEngine engine = new InternalEngine(config)) {
+                engine.reinitializeMaxSeqNoOfUpdatesOrDeletes();
+                engine.recoverFromTranslog(translogHandler, Long.MAX_VALUE);
+                assertThat(getDocIds(engine, true), equalTo(docs));
+            }
+        }
+    }
+
     public void testOpenSoftDeletesIndexWithSoftDeletesDisabled() throws Exception {
         try (Store store = createStore()) {
             Path translogPath = createTempDir();