PS: I don't think the change you linked to is what caused this, as that one is related to the 3D model folder, not the footprint folder names..
If I were to guess it sounds like the footprint association (EEschema/CvPCB) has stored some entries that can't be found anymore.
PCBnew > Preferences > Footprint Libraries Manager..
Find the footprint library NickName that now contains the Resistors_ThroughHole.pretty or whatever it's called now.
Then off to EEschema. Start CvPCB. It should have the new NickName that you found out earlier listed on the left.
Is that so?
Now you have to re-assign the footprints which still point to the old footprint library.