Auto-apply sent the wrong CV version

Auto-apply locks your default CV at the moment a run starts, not at the moment each application is sent. A run that began before you changed your default will use the old version for every application in it, including ones sent an hour later.

What you can do about applications already sent

Applications less than 24 hours old, to employers who have not yet opened them, can be superseded: open Applications → Sent, select the affected ones, and choose Replace attachment. The employer sees only the new version. Past 24 hours, or once opened, the file is part of their record and cannot be swapped.