Alternator replacement (service & policy question)

Back in June, I was on a road trip, and my alternator failed. Being an easy repair, I would normally do this myself, but since I was miles from home and it being a Friday afternoon, I had little choice but to have it repaired at a local major chain automotive place. Many weeks later, I had the typical squealing from a loose belt on start-up. I noticed that they left a nut off of the bottom alternator bolt, so the alternator had shifted position so it was at a slight angle. I found the right nut, and replaced it, but now it sounds “gravelly” like the alternator bearing was damaged by not being aligned correctly with the belt. I’m nearing the end of the 6-month warranty on parts & labor, so I’m thinking of bringing it in for a replacement.

Can I tell them I replaced the nut, or should I not say anything? I don’t want to void the warranty by having corrected their oversight. Looking for the best course of action from the service techs out there.