I was using the simulator, but I don’t think that is the problem. I just went in and manually deleted the folders and tried the script again and it is working. Sorry about the bug report!
The error was in the Momentic IDE, I told it to delete the project and the files, but it didn’t and when I ran the script and imported the files it had a weird mix of the last version plus the new version and got confused. I won’t trust that IDE to delete again, it also throws errors when you try to delete projects.