I had an EPiServer installed on my development machine (WinXP Pro) to the IIS root dir. As WinXP Pro only supports one root, I had to install it into Default Web Site. But when I uninstalled the EPiServer instance, the uninstaller deleted all files under wwwroot, even my other non-EPiServer projects which were installed in virtual directories under the Default Web Site.
This is a very serious bug in my opinion!
Jonas Hilmersson