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...
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.