https://bugs.winehq.org/show_bug.cgi?id=48312
--- Comment #2 from Clinton H 49studebaker@gmail.com --- (In reply to Nikolay Sivov from comment #1)
One issue is that winecfg itself is running in prefix you're about to remove. Various projects that help to maintain prefixes/wine builds are running as regular applications, so it's not a problem there.
From usability perspective this does not seem to be easier, you'll have to set WINEPREFIX, then run winecfg in it just to remove it, as opposed to just removing it.
I meant to say, it would delete the windows installation(.wine folder) and then create a new .wine folder.