We use usergroups (our admin team was on one) Our entire Admin team was deleted, and the skin I was using removed.
Best to start with the basics, how many adminstrators do you have on your board? So far deleting a usergroup, users and removing a theme are all actions a user with administration rights can do.
If you have more than one administrator, get all the administrators to change their passwords. Sounds a bit basic but it looks like a bit of animosity going on between the two sites and it could be possible that through some form of social engineering someone has managed to either get their username changed to administrator status or they have the password of one of the administrators.
Check to make sure no other username has administrator status. All that sort of thing, just eliminate it all as possibilities.