It is quite common to only sync with the Mix track(s) during editorial knowing that there is a downstream post process. Pro Tools has a feature to do track selection when conforming to get access to the desired track when conforming from the original files. There is functionality in the AutoSync window specifically designed to isolate any range of tracks from the incoming audio when syncing. Should the editor ever need to go back to an ISO track for whatever reason, it is a simple two match frame process. One from the record monitor to load sync clip, turn off V on source clip and hit match frame again on source and it will bring up the sound file at proper position on the MIX+ISO track file.
This does not mean that Media Composer can’t do a better job of preparing a timeline when sending over to a sound post process when working with Mix track only, but today it is handled in Pro Tools. And there are several designs I can think of to make this a much better process. But if you are working in something other than Pro Tools that may not have this feature, then editing with all the tracks may be the better way to go.
As far as your current situation, you can always subclip the sync clip with only the desired tracks in them. You cannot modify the tracks as suggested on the Avid Community forum. That can only be done on master clips. As far as already edited timelines. just delete the audio tracks that have the ISO provided no other audio events have been added to those tracks that you want to keep.
Michael