A couple of things I want to add: If, like me, you are decapping and cleaning cases before resizing, and if you are not doing this in and ultrasonic cleaner or with stainless steel pins, you can get corncob or walnut in flash holes that normally is pushed through them by the decapping pin on the sizing die, assuming you leave it in place. I had one decapping pin break on stuck media years ago, but only the one. I concluded that it had protruded just enough to deflect the pin to the side, where it hit brass. But usually the pin ensures a clear hole.
Where the clog issue has occurred for me is on brass I have lubricated for sizing and which I subsequently clean off with corncob in a vibratory tumbler. For me this is not about powder contamination, but rather is about ensuring lube inside the necks doesn't affect bullet pull. I was at a gunshow awhile back and bought a bag of corncob that is 10/14 grit size. Normally we use 20/40 grit in cleaning cases (see photos, here). The 10/14 I have is just too big to fit into a flash hole and stick there, so that doesn't happen and is one way to keep it clear.
Another point is that recently we had one stainless pin user put up a photo of two stainless pins wedged side-by-side in a flash hole. That is unusual, as the pins are usually the 0.041/0.047 diameter range diameters and so a hole at least 0.082" should be required for that to occur. Most are about 0.069 (Lapua Palma 308W cases) to 0.079". However, some flash hole diameter uniforming reamers are 0.081", and that means that if you don't go perfectly straight in when using it, it could wobble open wide enough for pairs of the 0.041" pins to lodge in there. If you buy the 0.036/0.041 diameter pins by mistake, that wedge could happen, too. That sort of jam is something I definitely would not want in the path of the primer flash, nor would I want them shooting down my bore. They also could conceivably set off a primer during priming if they protrude into the pocket. So, check that no such jam is present if you are using SS cleaning.
Finally, though MG showed no significant difference in his sample with pistol cartridges, that does not mean a high power rifle is not going to have sensitivity to the presence of flash hole debris. The issue is not muzzle velocity but ignition timing. If ignition starts an extra millisecond late, small vibrations due to the striker or small gun movements due to trigger slap all have more time to affect the exact location of the muzzle at the bullet's moment of exit. This could introduce stringing, even with matching velocities coming out of the barrel. It would be an interesting experiment, but it's the kind of thing that will affect one rifle and shooter combination more than another, as well as one load more than another, so it might take a lot of shooting to measure the effects. I think it's easier just to inspect and keep flash holes clear in the first place. Even if it all turns out to amount to nothing, introducing additional variables has never been shown to be helpful.