I included all of the original .swf flash files in the DVD_ROM folder. I would recommend omitting these when you burn the DVD. you get all of this footage on the DVD video anyway (that was the point of this DVD). I just included them originally in the DVD_ROM folder on the dual layer version because I had some room left and the files are relatively small. Removing those should clear up a bit of space for you. You can keep these on your hard drive or just get rid of them. I would recommend NOT re-encoding the DVD to be able to include this material on the DVD. It would degrade the video yet again.
I hope this answers your question. Let me know if you have any more. :)