I deleted the exported zip file that was placed in my exported templates folder and of course it still shows in Visual Studio\'s \"Add New Project\" dialog. I expected that but
At least for VSIX templates, the official way using VS2010 simply works:
Tools->Extension Manager...->Installed Extensions->Templates->$yourTemplate->[Uninstall|Disable]
Tools
Extension Manager...
Installed Extensions
Templates
$yourTemplate
[Uninstall|Disable]
If that works for you in the first place, you don't have to mess around with different folder layouts.