If you *permanently* alter the configuration then you need to notify ATF. This does not require a new stamp.
If it's an AR and you have it registered as a 11" 5.56mm and you decide to get a 5" 9mm upper for it you wouldn't need to notify ATF so long as you kept the 5.56 upper. If you got rid of the 5.56 upper and wanted to dedicate the lower to 9mm then that would be a permanent change that you'd have to notify ATF of.
Actually, it's not a requirement that you notify the ATF, it's just recommended by them, and a good idea so that the info regarding your firearm in the NFRTR is accurate.