I see. You might want to check "File" -> "Preferences", tab "General" option "Number of Steps of Undo". If that says "0" you cannot "Save" (but "Save As" should be still available. Aside from that deleting yEd's profile directory to reset yEd to its factory defaults might help. (If you have heavily configured yEd to suit your needs, moving the directory contents to another directory for later "restoration" might be a good idea in case you decide you want your old settings back.)