Update: I fixed the problem by reverting to a former backup and start the upgrade again.
The only things I changed between yesterday and today were:
- Renamed the Site Feedback standard category and slug, and put it under another new parent category.
- Renamed the Staff standard category and slug, and put it under another new parent category.
- Renamed the Lounge standard category and slug, and put it under another new parent category.
- Renamed Uncategorized via text edit (as proposed in the warning text) and slug, but left it as a top-level category.
Is it not allowed to make any of the changes above?