Recently I was refactoring a SharePoint project and wanted to be able to move the Resources mapped folder to a location external to my SharePoint project. In case you're wondering the reason, I'm working with both SharePoint 2007 and 2010 and I'd like to be able to consolidate as much code as possible.
Here are the steps I took:
1) Add the mapped folder to the SharePoint solution
2) Move the folder to the new, external, location
3) Create a symbolic link to the mapped folder and point it at the original location of the mapped folder using mklink (http://technet.microsoft.com/en-us/library/cc753194%28WS.10%29.aspx)
After these steps the Resources folder should still show up in your SharePoint solution package even though it's actually located outside the solution.