If you don't get stupid with the flute depth and try to make the barrel weigh somthing that it shoulden't then you should be OK , but your smith or whoever flutes it need to lap it well after or you could end up with some loose spots in the bore , its a alot safer bet to flute a cut rifled barrel after its done than a buttoned as they are less likely to have stress in them. I have seen and heard of both types of barrel both shoot as well after fluting and also being ruined after fluting.
My advice would be either to ship it back to Rock and have them flute it or to a smith that is going to take care in the job and do a good lapping job after word.