The issue is caused because the server paths have changed (something Rockbox Utility can't do anything or know about) and old files lying around. It has been fixed on the server (nothing I can do anything about except telling the server admins), and new versions of Rockbox Utility will use the new file paths, removing this issue completely. The state has been noted in the tracker issue I've linked earlier, so it was clear that it still persisted on 7th.