I think what happened, is the mod was loaded in a earlier version where a migration wasn't done properly, then saved again. It's hard to tell exactly what went wrong...
For migrating the project to a new save, if you can successfully load the mod in one of the later versions, it should be possible to export the entire project to a string and import in another project.
If that still doesn't work; please share a save, and I'll see what I can recover from it.
Maybe this can be automatically recovered in future mod releases.