You can use File/Import/Guvnor/Resources from Guvnor to get latest version of files into your eclipse project.
However if you delete them using eclipse, they dissapear from guvnor and you're not able anymore to import them, but they are still there somehow - govnor will not accept the same file anymore saying "already exists"...
I guess it's a feature protecting depending items from loosing their data...
As I understand it, the recommended way is to develop a resource package in clean guvnor and then transfer the whole package and deploy it...
I'm new here and still learning so hope I'm not wrong too much :)