It does appear that there is an issue with subdirectories not being created on iOS when restoring a backup now, which is most likely the source of the problem. I already submitted version 3.8.40, but once I have a fix in place for this, I can include it with the next update. If you uncheck that option though, MobileSheets should not create subdirectories and should be able to load files without an issue. I did test that and it worked fine for me. In fact, even when it didn't create subdirectories even though the option was enabled, I still could load songs without any problems. Please note that if you created custom subdirectories under the storage location, MobileSheets will try to honor those, so if you are seeing some songs still looking for subdirectories, that's probably related. I would need to see an example path of something that isn't loading properly for you though.
Mike
Mike