https://bugs.winehq.org/show_bug.cgi?id=49767
--- Comment #12 from m0rvj johnpgoodman@gmail.com --- I asked the devs: The other most troubling bug we have is that when running an update the user, docs and data files all get wiped so everything has to be downloaded again. I'm finding it extremely hard to track down. It would be great if you can think of anything which might help us fix it though.
Their answer: I can't imagine what's causing this. To the best of my knowledge, our Windows uninstaller does not delete the Docs folder (to avoid unnecessary hassle if someone's "uninstalling and reinstalling" to see if that fixes things (Tip: it doesn't)).
If it were me tracking this down on Windows, I'd use procmon to watch for all file access to that folder and see which process and thread is calling DeleteFile[A/W] on that path. Can DTrace on Linux do something similar...?