Do you rely on Time Machine? Drop to the shell right now and try "tmutil compare -n" to see which files are not making it onto your backups. For me, Time Machine randomly ignores certain files, for no discernible reason. Files that have sat on my disk literally for years will never get backed up. It's happened to me on two different Macs, and I've lost data because of it.
I ran into the same issue. After a restore from my time machine backup, I discovered that some files where missing (with no apparent pattern). Fortunately, I had a non time machine backup, but pheew that was a close one...
I discovered it when visiting an old project after a whole OS wipe-and-restore from TM. A week later I found that 'git' wouldn't recognize a project dir due to some missing pieces. I had a 2nd TM drive, and was able to manually restore files.
For my other machine, no such luck. I had a 2nd backup offsite (Backblaze) but it was months before I noticed the damage, and so the old files were no longer available via the offsite. I think the worst part is not knowing what you've lost. I have thousands of music and photos on that machine, and every once in a while I come across something that's gone.
