Nope, the prefix will be preserved if you remove and/or update Wine. If you change Wine versions, then upon osu!'s next start, you'll get a quick message about the prefix updating and then it should start.
Chaosemerald wrote:Not really related to osu!, but I just realized that the version of Wine in the Ubuntu repositories is really old (1.6.2) and I want to install latest version of Wine Staging using the official Wine PPA for Ubuntu. Will the prefixes disappear, if I uninstall Wine?
Also, osu! is apparently installed in a folder in my downloads folder. Will that go away too?