In my last American Hunter magazine I read an article on the effects on accuracy by purposely damaging the muzzle of a rifle barrel in differant ways to see how much it affected the accuracy and one of the tests was to drill the bore a bit oversized down about 3/4in. and it did have a substantial effect on the accuracy. My question would be does the overboring of the last 1/2in. or so that is done by many manufacturers of muzzleloaders to assist in starting the bullet have any adverse effect on the accuracy?

If the process was done with precision, I don't think there'd be much of a problem. The installation of a muzzel brake or flash suppressor is similar, and watching a couple DCM shooters practicing over the years, it doesn't hurt THEIR shooting a bit.

On some military rifles the armorer would counterbore the last inch or so of rifling to restore accuracy due to the damage to the muzzele from overzealous cleaning. As long as the hole is bored on center and the new crown is even I cant see any negative effect on accuracy at all.

Done right, it's a deeply recessed crown and shouldn't be an accuracy problem. I'd want it a good bit larger tahn bore diameter, but have done that trick on a couple that have had damaged muzzles (tink of it as a short "bloop tube" or un-ported muzzle brake)..

In my last American Hunter magazine I read an article on the effects on accuracy by purposely damaging the muzzle of a rifle barrel in differant ways to see how much it affected the accuracy and one of the tests was to drill the bore a bit oversized down about 3/4in. and it did have a substantial effect on the accuracy. My question would be does the overboring of the last 1/2in. or so that is done by many manufacturers of muzzleloaders to assist in starting the bullet have any adverse effect on the accuracy?

There is a difference in relieving the muzzle of a rifle shooting the PRB and drilling out the rifling of a modern centerfire. The ML must have a crown or relief that will allow loading. However, IMO it can be over done.
I don't do deep reliefs but will put a taper on the lands for the first 1/4 to 1/2" on some barrels especially pistols to make them a little easier to load. J. Bairds's "Hawken Rifles" has a test firing of an original rifle with a "funneled" muzzle and it shot pretty well.
Blackpowder is not smokeless and PRB guns are different than the BPCR.
For example the deep "target crown" found on many modern rifles will cause a BPCR to throw fliers in 4-5 shots. The BPCR will shoot better with NO crown and the most I ever put on one is just a slight cut to angle the lands at the muzzle. This is allow a patch to re-enter in a slotted rod is used.

Dan

On some military rifles the armorer would counterbore the last inch or so of rifling to restore accuracy due to the damage to the muzzele from overzealous cleaning. As long as the hole is bored on center and the new crown is even I cant see any negative effect on accuracy at all.

Do you have documentation for this?

Dan

Look at a surplus communist block rifle such as a Mosin M91/M38/M44 that is in issued condition, it is very common for them to be counterbored due to muzzle wear.