Hi Philip,
There is no way to automatically make thousands of changes to thousands of profiles at one time on WikiTree. (This is one of the reasons that the GEDCOM FAQ stresses the importance of smaller, more manageable GEDCOMs and being very cautious about upload.)
This particular error was created because your GEDCOM had references to "repository" records in your GEDCOM, but those links were broken because the repository records did not exist. It's certainly an opaque error message and ought to be improved. And, as you note, it serves no purpose in the profiles.
I'm sorry I don't have better news for you.
Chris