Tread very, very carefully here, especially if you have a version of Encore before 2.0. Even if you have Encore 2.0…
Also note that if the original assets are gone, deleting the contents of the Sources folder will cause everything to be offline until you relink to the original assets, if they are still available.
Safest course of action is to do a SaveAs of the project, and then do any housecleaning on that version of the project, checking along the way to verify that the project is still intact, but at its smallest possible size. Once you have something that is satisfactory, archive that.