If you know Linux well, it may not be that large of a problem. I once switched motherboards and had no problems at all, except for the sound driver which was different on the new board.
One thing you may want to do is make sure you can get to a command prompt from the boot loader, instead of straight into GDM. That way, if you can't boot with the new motherboard, at least you can get to a command line and do whatever you need to do to get back up and running, aka: recompiling a new kernel.
Or, maybe FC has a repair or re-install feature that will take care of it.. I'm not sure. You may also want to post on the
Phoronix forums and ask there. The site editor uses FC exclusively and has likely had to do this in the past.