https://bugs.winehq.org/show_bug.cgi?id=41400
--- Comment #13 from winetest@luukku.com --- Prefix is a folder under your home directory. The default is named .wine. If you delete the directory wine creates a new one when you start wine.
All programs should have their own prefix.
You could for example compile your own wine, but setting that up takes sometime. You need to hunt lots of development files.