Actually, you don't need to delete them. They will be automagically removed when the exclusion is changed since they will no longer be seen as books. The problem is that your Kobo excludes .kobo/screensaver by default but it does not exclude .kobo/screensaver_old. I took a look at my exclusion setting and found that I had modified it a while back to keep screensaver.old from being synced. It's not pretty and could be better coded.
Code:
ExcludeSyncFolders=(\\.(?!kobo|adobe).+|([^.][^/]*/)+\\..+)|(screensaver\.old)
should prevent this from happening.