Did you update from an older nightly release? I think the nightlies have switched from using the old version 4 repo(s) with the old by manufacturer organization scheme to the new version 5 repo with symbol lib organization by function.
The problem might now be that it does not update your sym lib table. (This is by design. To avoid problems for users with personalized library setups.)
If indeed your libs look like they are from the new organization scheme (compare the libs in the system folder against the new repo) then delete the no longer existing libs from your sym-lib-table and copy the content from the sym-lib-table that is supplied with your kicad installation into your personal sym-lib-table. (or use the symbol lib manager)
The new symbol lib will work best if you also use the new footprint libs with it. (Otherwise all default footprint fields and footprint filters point to non existing footprints.) This will mean you need to remove the github plugin libs from your global fp-lib-table and exchange them with the libs that are supplied with your installation. (Either use the library manager/wizard to correct the lib usage or use a text editor to copy the parts from the fp-lib-table in your system directory to the one in your user profile.)
If you want to stay at the version 4 libs, then you might need to download them by hand. (And again setup kicad to use these.)
I wrote a short tutorial on how to install a specific version of the footprint lib. In kicad nightly (versions that use the sym lib table) the symbol libs are handled similarly.