if I understood well ... since I'm not the Almighty ...
You want sometimes, just delete the links and keep the files ...
But other times, you want to delete the links and delete the files too ...
So if you choose one or the other option of JD2, leave it as the default, if you will get an undesired result with some links / files ...
I do not even want to say it probably will not be watching the robot all the time ...
I think this topic, but started differently, going in the direction of this other topic:
http://board.jdownloader.org/showthread.php?t=47586