Pokemon-go – My Pokemon changed after caught

As long as you are using different google accounts for Pokemon Go the fact that you are using the same apple ID will have no impact whatsoever on the game.

If you have changed Apple accounts since you downloaded the app then you may run into a problem when the app updates as it will ask for the password of the account is was downloaded under.

You can simply delete the app and redownload it under your current apple ID in order to have it under your current Apple ID instead of the old one. The fact that two people are using the same apple ID won't have any impact. It only matters that you have changed it since downloading it.

I'd suggest opening a ticket with pokemon trainer club, not niantic. Apparently the PTC login goes to a different Nintendo/Pokemon Company server before going to niantic, as thousands of PTC-login players were locked out during server maintenance on launch week, while Google-login players were far better off, and many managed to play just fine.

TL;DR, see if Nintendo can help you out. Since these accounts can have money poured into them, there's probably a legal failsafe to prevent a server hiccup or an accidental deletion from completely destroying all account data.