If you want to purge everything you may want to demux first, may be using PGCDemux 1.2.0.5 m03.
You may rewrite GOP Timecode into demuxed .m2v so that other apps reporting from that TC are not fooled anymore.
Since you want a backup, no cutting is performed.
Then if it's gonna be freeware, you may want to remux using MuxMan 0.16.8.
http://stnsoft.com/
Final Checks/modifications using PGCEdit 9.3.
If I want to see what I'm doing I reauthor using DVDLabPro 1 or 2,
DVD RemakePro 3.6.3, Sony DVD Architect Pro 5.2, 6.0, 7.0.