I never get rust in my barrel or any other part of my rifle because I never use water to clean it. No water, no rust.

What do you use?

I use equal parts of Murphys oil soap, isopropyl alcohol, and peroxide. Iv'e heard that there was some controversy about it harming the bore, but Iv'e had no problems with it. I always wipe out the barrel after using it and then using bore butter.

I've never had a problem with rust either-AND I use nothing BUT water!! and NO petroleum/modern lubes EVER!! and I've been shooting muzzleloaders for over 20yrs.

Not sure about Murphy's Oil soap, but OTC isopropyl alcohol and peroxide both contain copious amounts of water.

I use nothing but water. It is readily available, inexpensive and absolutely the best solvent for black powder fouling. Follow up with a couple of patches coated in bore butter or soaked in lehigh valley lube.
I say lap out the bad spot and then keep it rust free using a simple, petroleum free, time tested rust preventative.