this wouldn't be a problem. Then the user would log in and get a message that the encryption key doesn't match his log-in key. He could then adjust the encryption key password in the personal settings, given that he knows the old password. Because most likely her wouldn't know the password he would contact the admin and ask what's wrong with his account. The admin then can solve the issue, e.g. be deleting the keys so that the system create new keys during the next log in. I think some admin interaction is perfectly fine in such a extreme corner case.

Alternatively we could check if the keyfiles folder is empty to detect if encrypted files exists or not. But then you could ask what while happen if the user doesn't have encrypted files in the files folder but in the trash bin and want to restore them? I think the safe way is to only allow password change if the account wasn't in use before. Everything else needs to be handled by the admin manually if really needed.