Hi
You're not the only person to have this issue, but I've never seen a clear single explanation as to why it happens, sometimes the fonts just get corrupted.
Josephur may well be correct, and getting you updates caught up will fix it.
But as a backup option, once you get the fonts all back in place, make a copy of the fonts folder and save it to another location on the hard drive.
If you find a font missing you can retrieve it from that folder, you only have to right click on them and select Install.
You can also select all of them and have the entire fonts folder restored, just tell it to not replace existing fonts and it will add all the missing ones or you can just overwrite the whole folder.
I do it because I have a zillion...