This is a known issue. This is the primary thread on the matter:
https://us.forums.blizzard.com/en/wow/t/pet-battlecollection-broken/681040
TL;DR: Submit ticket(s) to restore pet cap. Re-do quests to regain ability to fight pet trainers; GMs don’t have the ability to restore that. Developers have fixed what caused paid character services to break these account-wide unlocks, so services are safe to use (claimed) but no one has come up with a clean way to restore those affected.
Sucks, but that’s how it stands now.