Yup, that's essentially what I do, except I don't have all of the same software and hardware that you're talking about. For example, I capture using the video card, but as I'm capturing I route audio through my external sound card...a Soundblaster Extigy because I'm just not aware of how well my video capture card processes audio. Once captured, I'll use either Vegas or DVDLabPro to strip the audio off and save it as a .wav file. Then I will use Audition to tweek the audio...add some bass, remove some noise, whatever. Then when I author the DVD, I'll mux the audio back together with the video. As long as you don't whack or add any length to the audio track, they're still perfectly synched.
This is also similar to how I synch a better sounding audio recording to a video with lousy audio. I will just strip off the audio from the AV recording and then synch up the audio that is stripped off with the external audio source by either stretching or shrinking and accounting for any drop-outs on one or the other audio's. Obviously, the key here is that you never touch the audio that was stripped out because that provides your reference. Then on final muxing, just substitute the original audio with the new audio.