This is a lot to ask, but if you're feeling particularly intrepid you could try bringing out the big guns: Microsoft's SysInternals page has a program called Process Monitor. It makes a huge log of which program did what while it's running.
https://docs.microsoft.com/en-us/sysinternals/
If you run it (procmon.exe), it'll start up by showing a list of filters. Here's a page showing how to add a filter for file deletions.
https://mikeberggren.com/post/135351739546/procmon-delete
If add that and hit ok, then try to install Fleshcult in Steam, you might see an entry in the big list for something deleting fleshcult (and probably a ton of unrelated deletions besides). By double clicking on the entry you can find out lots of stuff about that program and what it thought it was doing.