Schema migration deletes internal indexes created at startup #10837

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Issue Description

At startup, performInitialization creates internal indexes, then updateSchemaWithIndexes() copies them into _SCHEMA. DefinedSchemas then deletes every index that is absent from the local schema and absent from isProtectedIndex. keepUnknownIndexes is false by default.

username_1, email_1, case_insensitive_username, case_insensitive_email, name_1 (_Role) and reqId_1 (_Idempotency) are protected. Indexes added later are not:

• _User / _email_verify_token
• _User / _perishable_token
• _User / _auth_data_<provider>_id
• _Idempotency / ttl

Two instances that boot at the same time (Cloud Run, several containers) both try to drop the same index. The first drop succeeds. The second receives MongoServerError: index not found with name [_email_verify_token] (Mongo code 27, IndexNotFound). In production, after 3 retries, Parse Server calls process.exit(1). Retries do not recover: getAllClasses() serves the cached schema, which still contains the index.

With a single instance, boot succeeds and the index is then destroyed. Email verification and password reset queries scan _User.

Steps to reproduce

1. Run Parse Server with a schema migration (schema.definitions) that includes _User and does not list the internal indexes above. Leave keepUnknownIndexes unset.
2. Start the server so performInitialization creates _email_verify_token and updateSchemaWithIndexes() stores it in _SCHEMA.
3. Start a second instance at the same time, or restart once so the migration sees the index in the cloud schema.
4. Observe the migration drop _email_verify_token. The second concurrent drop fails with Mongo code 27.

Actual Outcome

The migration deletes internal indexes created at startup. A concurrent boot fails with MongoServerError: index not found with name [_email_verify_token] (code 27). After 3 retries the process exits in production. Email verification and password reset queries no longer use those indexes.

Expected Outcome

Internal indexes created at startup stay in place. Dropping an index that another instance already dropped is treated as success.

Environment

Server

• Parse Server version: 9.10.1-alpha.15 (still present on alpha as of 27 October 2026, 9.10.7)
• Operating system: Linux
• Local or remote host (AWS, Azure, Google Cloud, Heroku, Digital Ocean, etc): Google Cloud Run

Database

• System (MongoDB or Postgres): MongoDB
• Database version: MongoDB
• Local or remote host (MongoDB Atlas, mLab, AWS, Azure, Google Cloud, etc): MongoDB

Client

• SDK (iOS, Android, JavaScript, PHP, Unity, etc): n/a
• SDK version: n/a

Logs

MongoServerError: index not found with name [_email_verify_token]

Mongo error code 27 (IndexNotFound).