hans,
To remove the rifling in your flintlock pistol will likely require a piloted reamer. The rifling lands are probably 0.008" to 0.010" deep or more. That's too much to remove using abrasive cloth on a drill spindle. You might try looking for a 0.625" (5/8") straight shank machine reamer. Make up some hardwood blocks to hold the barrel in a drilling vise. Use a drill press on it's slowest speed and plenty of cutting oil. Let us know how it works out!
John