by Mark Pearson.
I think Emma's on the right track -- nice thinking Emma -- and her solution is the way forward.
Why not do a manual backup on a single course before the 'System' removes all the enrolments (why does it do this? strange) and then see whether that fixes the enrolments/gradebook on restore? If it does then all you have to do is to have the System execute site wide backups before mass unenrolling.