Happens a lot to me recently.
So far I've noticed a pattern, happened after i press power button when a game is running, seems like steam doesn't close itself properly ? and this most likely causes it to remove libraries.
Running KDE.
edit:
My settings in kde:
Power Management->Energy Saving:
Button events Handling
When power button pressed: Shut downStartup and Shutdown -> Desktop Session:
Default leave option: Turn off computerWhen logging in: Start with an empty sessionNothing extracted yet.
Your system information
From time to time the "Steam library folders" are deleted from the program and I have to add them again. I use Arch Linux.
Make sure the libraries don't disappear. And it happens randomly, I haven't noticed any pattern. And it's very annoying to add them again every time, because I have several of them.