I can't really speak to underlying issue which seems to be something with the employee fare, but from my experience upfaring from a standard (non-basic) Y cabin fare to a J/F fare, the final ticketed fare is the one that is observed when it comes to changes, IRROPS, etc.

This is different of course from being on a Y fare and doing a single-seat upgrade option through the website/app after booking. Those can definitely create headaches when it comes to changes, especially on round-trip tickets.

Either way, sounds like a case of a rogue agent who never should have had the authority to downgrade you on their own.