Unfortunately Steam Cloud indeed sometimes messes up files, but this still happens rare, and usually under specific circumstances (e.g when mixing online and offline sessions). So maybe there is something else going on that causes the file loss in your case?
The only thing I can think of is three different people use this machine. That is why I turn off Steam cloud. It would start having sync issues after a couple switches so I shut it off. I think when we get an update (not blaming you, it is more steam) they turn sync back on. I forget about it and...
The good thing is it does not look like they actually delete the files just the index. I turn sync back on. Got in the game, checked the files and they were there. Quick as a bunny😁