Yes that’s correct, the stock ST DTH does not “check” for existing codes beyond the first couple of codes. Also if you try to program the same code over on the lock (no matter which slot it may exist in) the lock will fail the transaction. Since there is no way to delete an existing code without it showing up in SmartLocks (but you an do this app use the Basic User Code Management app which allows you to delete individual slots. [RELEASE] Door lock code/lock user management (create, delete and schedule codes) with automatic lock/unlock, custom user actions and SHM integration), you should overwrite the slot with a new code and then revert back to your old code for it to show up in Smart Locks.
As a best practice when migrating locks to a new setup or a new app you should clear all codes/reset the lock and then program them through the app. This would avoid “hidden” or “lost” codes from compromising your setup.