CLR will not have any adverse affect on 416 stainless. I've left barrel cutoffs, partially submerged in 100% solution for weeks. There was no visible difference between what was submerged and what was not. Just patch it out, brush with your typically bore cleaner, and resume like you would normally do. I'd be far more concerned on getting the CLR on things other than the barrel steel, so I think removing the barrel, while being a bit of a PITA, is wise