I think I did not specify properly in my last post.
First you will want to go to main movie.
I'm writing this with the Lionsgate re-release of My Bloody Valentine, which does have the theatrical and extended version on the same side (1 sided dual layer).
I'm presuming the rated version comes up when you choose main movie/ customize and you want to backup the unrated version.
If the rated version comes up first, you will have to go down on the Main Movie and unclick the rated version and click the unrated version. The Main Movie will not allow the rated version to stay if you manually clicked the unrated version. If the unrated version comes up first, then proceed to the next step.
Next, in your audio selection box, unclick all boxes except for the audio you want to keep. Then go to the closed captioning box. Unclick all the boxes so that no subtitles are chosen.
Then copy the main movie to your Hard Drive.
Before you do your transfer to your mobile device, use the transfer you just did to your hard drive, using that as your source. It should show the preferences that you chose on screen.
(In my transfer I chose 2 channel audio, no subtitles which showed on the DVD to DVD selection screen as I had selected.)
Then do your DVD to mobile device, as usual.
I hope this helps, and I wasn't too over specific. (I was actually working towards "tad bit"