Flash chat has never given me a problem

You will have to revert the navbar template which means you will have add your link to flash chat back but thats it.. ITs almost stand alone and Paul M's integration is all done by plug in so Ive never had problems with upgrades concerning flashchat.

Not saying it wont have a problem just think its unlikely.
Paul is SUPER fast about updating his mods too.
So if its just flash chat you want... I'd say your safe!