remuxing encoded video with original vobs ?

[radius]

Hi,
so i'm looking for a way to remux a ntsc (film) video i'll encode in the original vobs, so replacing original vid with encoded one, I extracted chapters frame list (from ifoedit or pgcedit) but when imported in cce and compared to chapters in pgcedit it doesn't match (i compare the image) so I can't get cce to encode the extact same cells :o, is it a problem for vobblanker ?
If yes i could actually encode cell by cell like dvdrebuilder do but, I'm not sure how to rebuild the complete video "pulldowned" after.
Please guys let me know your thinkings.
Thanks

[radius]

ok as i never used vobblanker before i just realised i can't just replace one stream but i need to rebuild the all video + chap + audio etc then replace the original with this (right ?), what I would need is something similar to dvd rebuilder, i can encode cell by cell but can someone tell how is dvd rebuilder remuxing and fixing the stuff ? is there a tool to specialy do that ?
thanks