That's not what the help section said. Deleting ~/.wine basically deletes *all* installed Wine apps that were installed in that directory (the directory is also known as a Wineprefix). It's still safe to do, system-wise. If you want to keep your other installed Wine apps, just go into ~/.wine/drive_c/ and find the directory/ies where the app is installed. You can remove the directory quite safely - it'll probably just leave around some dead links, no longer used DLLs and some junk in the registry, just like in Windows.
