Everything in my brain, is wanting me to tell you, that you need to re-install the OS. In effort of doing so however, I truly hope that your drive has been formatted to EXT4 GPT.
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Sadly, one thing that comes to mind that can cause such a mysterious failure is - a sign that the SSD or HDD is beginning to fail...
Thats always the worst situation, I've gone through that with old mechanical drives, that had too many bad sectors, and they were like mornings french toast. Oddly enough, I still don't have issues with the very first SSD I bought, still going strong, used as an external drive now. I also make sure to only buy Western Digital or Samsung drives, for reliability sake.
I had meant to return to this thread and suggest:
@i.guigo, you might run a S.M.A.R.T. (test) on the drive to check for signs of failure. Too many things going on at once and I only remembered when I got an alert on this thread...
An unfortunate reality is that a S.M.A.R.T. can show an established flaw, but not necessarily flag initial signs of failure. So, even if it passes; plan Data Back Up's with vigor.