Just as a point of information, I ran into this very problem (lost my pocket pet portal, capped at 1000 pets but had more than that, had to relearn pet battles, etc.) on both the Beta and PTR and I reported it. It wasn’t an addon or UI issue on there (didn’t have addons and did the full UI reset there too). It was a problem with my account as far as I could tell. Perhaps it leaked onto the live realms with the prepatch?
EDIT: There is a bug report out on it as well in the forums: