I think you should be fine, and if not would you consider letting him have the site since he has been there so long already and you look for another? If it came to it they would probably compromise and ban one of the accounts so the other could remain active.

I really don't think that will happen though. Having modded and seen mods on many sites this sort of thing happens quite a lot The fact that you have explained it should be enough. That is why they PM you first and don't just ban the accounts. They want to give you a chance to explain in case there is another reason.