Hi Neon. The Womble editors can do this - I used Video Wizard to recut the Terminator 2 'CDS' mix from the Artisan DVD, which didn't have a terrific bitrate to begin with so I wanted to preserve the original data at the very least. I did something like 30 edits overall to sync with the video, and the AC-3 file was then just rebuilt with the alterations.
Have a look to see if there's a trial version or something: http://www.womble.com/index.html