Computers can do some strange things. I have a feeling that the problem lies not with steam but possibly your computer. I would definitly run a virus scan just to make sure nothing is messing with your files. I highly doubt there is, but when I see stuff like that happen on my computer I run a good scan with Malwarebytes.
My only other idea is that you may have your computer to uninstall unused programs or files. I have no idea how your computer is setup, but the virus idea, and accidental. uninstall are my only ideas.
P.S. I had issues with steam before where it said I didn't even own half of my games. I went in and made steam redownload its updates and let the computer run for a few hours. When I came back all was well. If you go to steam support there should be instructions on how to delete the steam blob file(also some other things needed to work) so steam updates again.
Just some things I would personally go and check.
