It’s a hack, but this worked for me:
- Set the Current version of the model in Xcode to one that you want to keep
- Remove the .xcdatamodeld from your project (Right-click -> Delete -> Remove Reference Only)
- Show the contents of the .xcdatamodeld package in the Finder (Right-click -> Show Package Contents)
- Delete the .xcdatamodel file(s) that you don’t want anymore
- Re-add the .xcdatamodeld file to your project
This eliminates the need to manually modify any of the project metadata files.