The ATF doesn't care even if you have the gun on the schedule incorrectly, because as others have said, they don't care if the firearm is on the schedule at all, only that the trust is valid. I have actually sent the same original schedule A that contains one dollar for all of my Forms, even after several other approvals on that trust. They really don't care what's on the schedules or even if they are receiving the current schedule because I've updated the schedule since building some things and I still send them the old one because it's already in the PDF file.
Correctness on the forms and a legal trust are all they want.
BUT... to answer your question about how to correct it... You simply need to edit the Schedule A and print a new one out, and sign it and date it. No need for the notary (at least, not here in PA, other places might vary but I have never heard of needing to have the Schedules notarized after a change). The most current version of the Schedule A supersedes the older ones. You can keep or discard the older versions, I keep them for the hell of it.