This would essentially turn the command module and the rest of the vessel into debris, allowing you to revisit it later if you want either recovering it, encountering it or just pressing the 'reactivate command' option to convert it back to what it was if you need to use it again, rather than just deleting it from the game via the 'terminate'. This would help to clean up the tracking station view by not displaying things you dont want to use anymore but may want to preserve for posterity, especially usefull during the late game when things can get a bit crowded with old vessals, stations and probes