https://bugs.winehq.org/show_bug.cgi?id=22974
--- Comment #11 from Adam Bolte abolte@systemsaviour.com --- For as long as I can remember, I always have to run winecfg, navigate to Desktop Integration, and untick "Link to" for every path whenever I load a new Wineprefix after changing Wine builds. I vaguely recall that even just applying a patch seems to cause your customisations getting overridden.
This is currently the most annoying bug in Wine that's not compatibility-related.