I'm trying to follow what you are doing but I might have gotten lost. Usually what I do is I edit my video and once I have "picture lock" meaning I'm not going to change anything in the sequence I bounce out my audio stems which could be two or three dialog tracks for example. Then I take those into Adobe Audition and apply any EQ and compression and other effects and export those back out. Then I import those files back into my sequence and mute my original audio.
I'm with Gerik. I don't see the problem ... I wouldn't be even touching the audio until I'm done with the sequence. And depending on how much work needs doing I may simply use the audio workspace & Essential Sound panel, or bounce the track to Audition, re-import.
But that way I'm not wasting time on material that's not in the edit.