Each Square Enix account can have up to 8 service accounts (8 different subscriptions with the same login details), so if she clicked create new, she's either added it as a different service account, or she's created a completely new account with new login details (which is why you can't see the other character).

When in the Mogstation, you can select which service account to look at from the tabs at the top of the page:



If you're not seeing these tabs and/or there's only 1 service account, then that means the old character is on a different account/different login details. If you are seeing this then in game you switch service accounts using the "Data Centre" option on the main menu. After you select one, if you have multiple service accounts it then prompts you for which service account to use.

SE have forms for both situations though (according to the forms, it may take up to 2 weeks to fix):

Game registered to wrong service account (same main account):

NA: https://support.na.square-enix.com/c...82&la=1&daxx=2
EU: https://support.eu.square-enix.com/c...82&la=1&daxx=2

Game registered to new account instead of existing one:

NA: https://support.na.square-enix.com/c...82&la=1&daxx=1
EU: https://support.eu.square-enix.com/c...82&la=1&daxx=1

There's a bit about unlinking PS4 ID too, but sorry no idea about that part.

Hopefully you can work out which you need, but otherwise might be faster to call SE so they can confirm what you need (these forums are only for players to help other players, there's no official support here).