After zeroing a muzzleloader then cleaning it...will it change the way it shoots any substantial amount when you shoot it through the clean barrel?

Some rifles make no difference ... clean or fowled. Others can throw off as much as two inches. The only way to be sure is shoot on a clean barrel. Swab it clean and shoot on a fowled barrel. See if there is a big difference.

+1 with cayugad. See how your rifle shoots with a clean barrel and a fouled barrel. Some will make a much larger difference than others.

i have found it depends on what bullets i am shooting shockwaves,hornady's ect i would get a flyer on the first shot out of a clean barrel with my apex.but since i have went with the powerbelt platiums it doesnt effect my accuracy they shot the same very clean or a swabbed barrel.

I have just started using this method this year and testing is so far so good. http://www.eabco.com/MuzzleLoader02.htmIf it has been cleaned I take the clean oiled barrel and clean the oil. Wipe with a T7 patch then a dry patch. So far my first shot has been in the group with the other shots on my Omega and my Dad'ss Optima. It will take more time to make it conclusive with me but looks promising