Ninosdemente,
I have encountered a couple of examples of deburring flash holes helping over time.
Twenty-five years ago, my M1A's original barrel would shoot 0.7 moa consistently with my handloads built with IMR4895 and 4064, Brigadier 3032, Reloader 12, and a few other stick powders I tried. One year I decided to try Accurate 2520 because, being a spherical powder, it metered well. My groups opened to 1.2 moa and would not tune down. Then, on a whim one day, I tried deburring flash holes and the 2520 groups shrank to 0.7 moa same as the other powders. Knowing more now, I might have got the same result going to a magnum primer, but that barrel is long sice shot-out, so I can't make the retro-comparison. I can only say it was apparently the case that deburring flash holes helped a harder-to-ignite powder work up to its potential. Of course, I then went back to stick powder hoping for a similar improvement, but saw none. 0.7 moa was being limited by the gun or the shooter's ability with iron sights and the long, heavy trigger at that point.
Another instance is with once-fired crimped primer brass. I use the Dillon 600 swaging tool to remove crimps. It backs up the head of the case with an anvil on the inside while swaging the crimp out. I discovered that the anvil can bend the flash hole burrs over the hole, obstructing it. This is an inconsistent issue, but one that occurs often enough that I have to watch for it. I either have to drill such holes clear or deburr before running them through the tool.