diff --git a/.changeset/quiet-pianos-fix.md b/.changeset/quiet-pianos-fix.md
new file mode 100644
index 0000000..d16144e
--- /dev/null
+++ b/.changeset/quiet-pianos-fix.md
@@ -0,0 +1,5 @@
+---
+'@electric-sql/d2ts': patch
+---
+
+Fix SQLite index compaction dropping data when a version advances to itself under an incomparable frontier
diff --git a/packages/d2ts/src/sqlite/version-index.ts b/packages/d2ts/src/sqlite/version-index.ts
index 4729b50..dba9891 100644
--- a/packages/d2ts/src/sqlite/version-index.ts
+++ b/packages/d2ts/src/sqlite/version-index.ts
@@ -542,6 +542,12 @@ export class SQLIndex<K, V> {
         const newVersion = oldVersion.advanceBy(compactionFrontier)
         const newVersionJson = newVersion.toJSON()
 
+        // Incomparable versions can advance to themselves; moving those rows
+        // would insert into the destination and then delete it.
+        if (oldVersion.equals(newVersion)) {
+          continue
+        }
+
         if (!versionGroups.has(newVersionJson)) {
           versionGroups.set(newVersionJson, [])
         }
diff --git a/packages/d2ts/tests/version-index.test.ts b/packages/d2ts/tests/version-index.test.ts
index cb100fb..d2835ef 100644
--- a/packages/d2ts/tests/version-index.test.ts
+++ b/packages/d2ts/tests/version-index.test.ts
@@ -330,6 +330,28 @@ function createIndexTests<
         expect(result).toEqual([[10, 2]])
       })
 
+      test('should handle compaction with incomparable versions', () => {
+        const version1 = v([1, 0])
+        const version2 = v([1, 1])
+        const version3 = v([2, 0])
+
+        index.addValue('key1', version1, [10, 1])
+        index.addValue('key1', version2, [10, 2])
+        index.addValue('key1', version3, [10, -1])
+
+        const frontier = new Antichain([v([1, 2]), v([2, 1])])
+        index.compact(frontier) // [1, 1] -> [10, 3] and [2, 1] -> [10, -1]
+
+        const result1 = index.reconstructAt('key1', v([1, 2]))
+        expect(result1).toEqual([[10, 3]])
+
+        const result2 = index.reconstructAt('key1', v([2, 1]))
+        expect(result2).toEqual([
+          [10, 3],
+          [10, -1],
+        ])
+      })
+
       test('should throw error for invalid compaction frontier', () => {
         const version = v([1])
         const frontier1 = new Antichain([v([2])])