I've got 6950s and 6970s.
RBE warns on certain changes that the native drivers may stop recognizing the card.. and someone else mentioned after a certain RBE edit even aticonfig wouldn't find the cards.
Are you using a signed 'rbe' excerpt from another card (~1kb) to get around that?
As already mentioned, make sure you make a backup of your existing BIOS. atiflash has a built-in command (-s X filename).
I don't bother with the RBE signatures, etc - I just change my clocks under Additional Settings with relatively good luck so far.
The only "issue" (really not an issue) is that on reboot after flash, Windows did infact not recognize the card.... and I had to go through letting it re-detect and put the drivers back in place. Occasionally, it would do that every 3 or 4th reboot. I stopped using Windows whenever possible....

PS - for the record, ^ the above only happened on one Windows PC and a buddy with an identical card doesn't have that problem.