Looking at the code SharpDevelop searches the SharpDevelop\data\templates path and any paths defined in the .addin files. So there's no support for custom templates in different folders.
If you're using the installer for 2.1 it does not remove any files or folders that it didn't create. However it could be possible that a new template is added with a newer release of SharpDevelop and it has the same name as one of your files.
I've added a feature request to implement custom template folders to the bugtracker.