Tom, we tried to be more explicit about what Shozam does. Each time Shozam generates a modified gallery, it will delete folders which it considers not needed any longer so it can get rid of any deleted albums. It first evaluates which are the folders it needs to have in the root, based on the active gallery settings, and then it will delete any other folders it may find in the root. This happens each time regardless of the "generate modified files only" checkbox state.
This will afect you only if you copy some other folders into the Shozam gallery root. Outside files placed in the root will be OK, just not folders. If you really need to have some external folders, the hack would be to palce them into one of the Shozam generated folders, like in the "scripts" folder.