I've fluted finished barrels before.
Not hundreds of them, but quite a few in a variety of brands, contours, and calibers.
I've yet to have one "go south" on me. The procedure is important. Take a big snorty cut and you are liable to generate some heat and a significant amount of stress removal all at one time. Its reasonable to assume then that the bore dimensions alter slightly and the gun is now prone to shooting poorly.
So. . .
Take smaller cuts and run it over a few passes and it seems to work fine. least that's been my experience. I change locations every pass and work 180 degrees from the previous cut. Cutter selection also makes a difference. I never use a ball end mill. No matter what spindle speed the tool is at, the center isn't turning. This means it's not cutting as it has no surface speed. It's deforming the material or "peening" it. you can see this because the tool marks will leave a slight line at the root of the flute. I cannot help but feel that induces stress as it'd be no different than if I took a hammer and punch and peened the barrel all over the place. Displacing metal introduces stress just like cutting on it does.
I use a profiled key type cutter and work on the side of the barrel. It complicates sets up a little since the machine is a vertical mill, but with a little thought it can be done without too much head scratching. A 4th axis certainly makes life easier too.
Several well established barrel makers will flute a barrel that is finished. If they can do it, it's stands to reason that others can too.
Good luck.