Before you start trying to re-tap the threads, try using a bore brush of about .25-30 caliber to put in the threads and twist it around to get any debris out of there.
The other thing that you want to do is go to Lowes or any other hardware store with the nipple. In the screws, nuts and bolts section is a thread gauge for both metric and SAE.
See which gauge the nipple screws into. That is the thread pitch that you want to get.
The problem that you are experiencing has happened to me on occasion. I get that problem with by percussion rifles and the cap & ball revolvers.
Just recently, I experienced the very same problem with my Howdah pistol and Charles Moore percussion pistol. Both of them are made by Pedersoli.
When trying to screw the nipple back in place, it is a little difficult to get started at first. It almost seems like I'm cross threading the darn thing. Nevertheless, I take my time and ensure that I am, indeed, getting the nipple started correctly. I use the nipple wrench to slowly turn the nipple and making darn sure that I am not cross threading it.
It seems tight at first but once I make a few turns it goes in easy. I don't have any problem removing or replacing them later on.
The other technique that you will see some people suggest is coating the threads with anti-seize lubricant. I have been using white lithium wheel grease on all my nipples for the past 40 years. I've never had a stuck nipple.
For example, I don't remove the nipples from my cap & ball revolvers for every cleaning. IMHO, there is no need to do that as long as I have pre-lubed the threads with the white lithium wheel grease.
The white lithium grease is cheap and plentiful. You can pick it up at the hardware store while you are measuring the thread pitch of your nipple.