[Demongornot]

Ok, that mean I'll code it so, it detect duplicates when the files are added in the link grabber, automatically disable them and put in their comment that they are duplicate, leaving the user free to decide whatever or not he should download them or not, and it will only take into account file already in the download list with an option to choose between added and finished download to be added to the already downloaded link list.
Also I think I'll also make so that on first launch, if the option is enabled, and no downloads history have been already recorded, that he add every existing files to the list.
It will work through two scripts, one to add every freshly started downloads or finished downloads (user choice) into the script, and the other to verify added links.

I'll just have to experiment on multiple trigger reading and/or writing on the same file "at the same time" as I don't know how JDownloader 2 handle that.
Might have to create temporary files for each instance of the script and add all the downloads at a certain moment (when downloads are stopped and/or when ETA of all active downloads is big enough) or when JDownloader is closing, for safer writing into the main list though it would mean a third script and you'll need to close JD to update the list, but this is my backup solution.

For the red downloads, I'll have to experiment and search a lot to find how to do that, but I'll try, it will be better than disabling and commenting them.
For the DLC I never tried that and I completely ignore what this is, so I'll do the script without that first, learn what this is and depending of what this is and how it work try to make as you suggest.