diff --git a/src/main/index.ts b/src/main/index.ts
index cc30b7de..6716e5d0 100644
--- a/src/main/index.ts
+++ b/src/main/index.ts
@@ -181,29 +181,44 @@ else {
           = (store.preferences.get('storage.vaultPath') as string | null)
             || path.join(storagePath, 'markdown-vault')
         ensureFlatSpacesLayout(vaultPath)
-        const { hasMarkdownVaultData } = lazyRequire(
-          './storage/providers/markdown',
-        ) as typeof import('./storage/providers/markdown')
-        const vaultHasData = hasMarkdownVaultData(vaultPath)
-
-        if (!vaultHasData) {
-          const { closeDB } = lazyRequire('./db') as typeof import('./db')
-          const { migrateSqliteToMarkdownStorage } = lazyRequire(
-            './storage/providers/markdown',
-          ) as typeof import('./storage/providers/markdown')
 
-          try {
-            migrationResult = migrateSqliteToMarkdownStorage()
+        // Авто-миграция из SQLite выполняется только один раз. Флаг
+        // storage.sqliteMigrated персистентно блокирует повтор, иначе ручная
+        // очистка vault при сохранившемся massCode.db триггерила бы миграцию
+        // заново и возвращала удалённые данные.
+        const alreadyMigrated
+          = store.preferences.get('storage.sqliteMigrated') === true
 
-            store.preferences.delete('storage.engine' as any)
-            store.preferences.delete('backup' as any)
-
-            // eslint-disable-next-line no-console
-            console.log('[Auto-migration complete]', migrationResult)
-          }
-          finally {
-            closeDB()
+        if (!alreadyMigrated) {
+          const { hasMarkdownVaultData } = lazyRequire(
+            './storage/providers/markdown',
+          ) as typeof import('./storage/providers/markdown')
+          const vaultHasData = hasMarkdownVaultData(vaultPath)
+
+          if (!vaultHasData) {
+            const { closeDB } = lazyRequire('./db') as typeof import('./db')
+            const { migrateSqliteToMarkdownStorage } = lazyRequire(
+              './storage/providers/markdown',
+            ) as typeof import('./storage/providers/markdown')
+
+            try {
+              migrationResult = migrateSqliteToMarkdownStorage()
+
+              store.preferences.delete('storage.engine' as any)
+              store.preferences.delete('backup' as any)
+
+              // eslint-disable-next-line no-console
+              console.log('[Auto-migration complete]', migrationResult)
+            }
+            finally {
+              closeDB()
+            }
           }
+
+          // Помечаем миграцию как выполненную в обоих случаях: после успешной
+          // миграции и как backfill для пользователей, уже мигрировавших в
+          // прошлых версиях (vault с данными, но без флага).
+          store.preferences.set('storage.sqliteMigrated', true)
         }
       }
     }
diff --git a/src/main/store/__tests__/preferences.test.ts b/src/main/store/__tests__/preferences.test.ts
index 8f29cd26..2b1e76c8 100644
--- a/src/main/store/__tests__/preferences.test.ts
+++ b/src/main/store/__tests__/preferences.test.ts
@@ -170,6 +170,30 @@ describe('preferences store sanitization', () => {
     ).toBeUndefined()
   })
 
+  it('keeps persisted sqliteMigrated flag and defaults it to false', async () => {
+    persistedStateByName.preferences = {
+      storage: {
+        sqliteMigrated: true,
+      },
+    }
+
+    const { default: preferences } = await import('../module/preferences')
+
+    expect(preferences.get('storage.sqliteMigrated' as any)).toBe(true)
+  })
+
+  it('defaults sqliteMigrated to false for invalid or missing value', async () => {
+    persistedStateByName.preferences = {
+      storage: {
+        sqliteMigrated: 'bad',
+      },
+    }
+
+    const { default: preferences } = await import('../module/preferences')
+
+    expect(preferences.get('storage.sqliteMigrated' as any)).toBe(false)
+  })
+
   it('keeps persisted http settings and prunes stale values', async () => {
     persistedStateByName.preferences = {
       http: {
diff --git a/src/main/store/module/preferences.ts b/src/main/store/module/preferences.ts
index 73cd75ba..114462f0 100644
--- a/src/main/store/module/preferences.ts
+++ b/src/main/store/module/preferences.ts
@@ -58,6 +58,7 @@ const PREFERENCES_DEFAULTS: PreferencesStore = {
   storage: {
     rootPath: storagePath,
     vaultPath: null,
+    sqliteMigrated: false,
   },
   editor: {
     code: EDITOR_DEFAULTS,
@@ -307,6 +308,10 @@ function sanitizePreferences(value: unknown): PreferencesStore {
         'vaultPath',
         PREFERENCES_DEFAULTS.storage.vaultPath,
       ),
+      sqliteMigrated:
+        typeof storageSource.sqliteMigrated === 'boolean'
+          ? storageSource.sqliteMigrated
+          : PREFERENCES_DEFAULTS.storage.sqliteMigrated,
     },
     editor: {
       code: sanitizeCodeEditorSettings(codeEditorSource),
diff --git a/src/main/store/types/index.ts b/src/main/store/types/index.ts
index 7e6e43f5..af628c65 100644
--- a/src/main/store/types/index.ts
+++ b/src/main/store/types/index.ts
@@ -190,6 +190,7 @@ export interface MarkdownSettings {
 
 export interface StorageSettings {
   vaultPath: string | null
+  sqliteMigrated: boolean
 }
 
 export interface NotesEditorSettings {