diff --git a/.changeset/pink-moles-leave.md b/.changeset/pink-moles-leave.md
new file mode 100644
index 0000000000..c6aabb802b
--- /dev/null
+++ b/.changeset/pink-moles-leave.md
@@ -0,0 +1,5 @@
+---
+'@shopify/theme': patch
+---
+
+Fix `shopify theme dev --theme-editor-sync` to avoid deleting files during race conditions, especially when multiple changes come from an external process (e.g., AI coding tools)
diff --git a/packages/theme/src/cli/utilities/theme-environment/theme-polling.test.ts b/packages/theme/src/cli/utilities/theme-environment/theme-polling.test.ts
index 02b893d241..4576fba4a9 100644
--- a/packages/theme/src/cli/utilities/theme-environment/theme-polling.test.ts
+++ b/packages/theme/src/cli/utilities/theme-environment/theme-polling.test.ts
@@ -266,6 +266,33 @@ describe('pollRemoteJsonChanges', async () => {
       expect(fetchThemeAssets).toHaveBeenCalledWith(1, ['templates/asset1.json', 'templates/asset3.json'], adminSession)
       expect(fetchThemeAssets).not.toHaveBeenCalledWith(1, ['templates/asset2.json'], adminSession)
     })
+
+    test('does not delete file when it becomes unsynced during fetchChecksums call (race condition)', async () => {
+      // Given
+      const files = new Map<string, ThemeAsset>([
+        ['templates/index.json', {checksum: '1', key: 'templates/index.json', value: '{}'}],
+      ])
+      const themeFileSystem = {
+        ...fakeThemeFileSystem('tmp', files),
+        unsyncedFileKeys: new Set<string>(),
+      }
+      const deleteSpy = vi.spyOn(themeFileSystem, 'delete')
+      const remoteChecksums = [{checksum: '1', key: 'templates/index.json'}]
+      const updatedRemoteChecksums = [{checksum: '1', key: 'templates/index.json'}]
+
+      // When
+      // Simulate the race condition: file becomes unsynced during fetchChecksums
+      vi.mocked(fetchChecksums).mockImplementation(async () => {
+        themeFileSystem.unsyncedFileKeys.add('templates/index.json')
+        return updatedRemoteChecksums
+      })
+
+      await pollRemoteJsonChanges(developmentTheme, adminSession, remoteChecksums, themeFileSystem, defaultOptions)
+
+      // Then
+      expect(deleteSpy).not.toHaveBeenCalled()
+      expect(themeFileSystem.files.get('templates/index.json')).toBeDefined()
+    })
   })
 
   describe('deleteRemovedAssets', () => {
diff --git a/packages/theme/src/cli/utilities/theme-environment/theme-polling.ts b/packages/theme/src/cli/utilities/theme-environment/theme-polling.ts
index 342e0f2a9b..c8de412668 100644
--- a/packages/theme/src/cli/utilities/theme-environment/theme-polling.ts
+++ b/packages/theme/src/cli/utilities/theme-environment/theme-polling.ts
@@ -80,9 +80,21 @@ export async function pollRemoteJsonChanges(
   localFileSystem: ThemeFileSystem,
   options: PollingOptions,
 ): Promise<Checksum[]> {
-  const previousChecksums = applyFileFilters(remoteChecksums, localFileSystem)
+  /*
+   * Capture the current set of unsynced file keys to ensure
+   * consistent filtering between previousChecksums and
+   * latestChecksums.
+   *
+   * This prevents a race condition where a file saved locally
+   * during fetchChecksums() would be filtered out of
+   * latestChecksums but not previousChecksums, causing the file
+   * to incorrectly be deleted.
+   */
+  const currentUnsyncedKeys = new Set(localFileSystem.unsyncedFileKeys)
+
+  const previousChecksums = applyFileFilters(remoteChecksums, localFileSystem, currentUnsyncedKeys)
   const latestChecksums = await fetchChecksums(targetTheme.id, currentSession).then((checksums) =>
-    applyFileFilters(checksums, localFileSystem),
+    applyFileFilters(checksums, localFileSystem, currentUnsyncedKeys),
   )
 
   const changedAssets = getAssetsChangedOnRemote(previousChecksums, latestChecksums)
@@ -189,9 +201,7 @@ async function abortIfMultipleSourcesChange(localFileSystem: ThemeFileSystem, as
   }
 }
 
-function applyFileFilters(files: Checksum[], localThemeFileSystem: ThemeFileSystem) {
+function applyFileFilters(files: Checksum[], localThemeFileSystem: ThemeFileSystem, unsyncedKeys: Set<string>) {
   const filteredFiles = localThemeFileSystem.applyIgnoreFilters(files)
-  return filteredFiles
-    .filter((file) => file.key.endsWith('.json'))
-    .filter((file) => !localThemeFileSystem.unsyncedFileKeys.has(file.key))
+  return filteredFiles.filter((file) => file.key.endsWith('.json')).filter((file) => !unsyncedKeys.has(file.key))
 }