I know of an ex-NCO and an ex-Nav that both had fATPLs. They both had to do most of the military pilots' course again when they rebranched.
I would have thought that it would be a positive advantage if you went multis, but for FJ and rotary then there would be quite a lot missing from your training. That said, at the recruiting office having a fATPL must offer you advantage over the other candidates.
Good luck!
LJ