Many many times I have used a Redding Body Die to make minor adjustments to the case shoulder on loaded ammo. Also have used a Redding Type S Bushing Die, without bushing, to do the same thing. Works great.

I don't have any worries while doing it, but if you do, that's fine too.

I had my 223 rebarreled, and the new barrel had a real tight chamber. Much tighter than the original barrel. I had maybe 300 rounds loaded that would no longer chamber. Rather than pull them, I just ran them through the Type S Bushing Die, with no bushing, and it worked great and was a fast fix. They shot great in the new barrel.