@metalkramp it sounds like it may be easier for you to only use tags in this case, and use a custom plugin to display certain tags as if they are categories.
Categories drop-down empty after migration to 1.16.x
I've recently upgraded from 1.12.x to 1.16.x and I've done it first on a testing environment and, upon success, on production environment.
Today, after a few days from the upgrade, I've realized that on the production instance the list of categories from category-drop down menu, is completely missing either on front-end (typical case when you want to move a thread) and on back-end (typical case when you want to set privileges).
Production instance(left) Vs Test instance (Right)
I've no clue what could be the case and how to get it fixed.