Updating nightly might have updated the library.
This is one of the dangers of using nightly
If the libs have been updated to the new library organization, then nearly all symbols, footprints and 3d models have a different name or live in a different lib then before the update.
Footprints are cached in the pcb_new file format. So even if you update your pcb stays valid. (similarly the symbols are cached in the cache lib and can be "rescued".) There is no caching of 3d data.
To fix your problem i would suggest you install a version of the 4.x library somewhere convenient and point old projects to it. Part of this is explained in this FAQ post: https://forum.kicad.info/t/how-can-i-install-a-specific-version-of-the-footprint-library/9269