I just really feel like I need to add a few short things to this thread.
I believe you would get the results your looking for if you also export with “Create merged clips” (You do this in the exporting process of plural eyes.) This will give you two sequences, 1. with audio synced to the video with the original audio contained and 2. A sequence with the video and only the sound from the audio recorder.
As mentioned above, you can link your clips (cmd + L).
What I like to do, to “guard myself up” incase plural eyes screws up (which happens time from time) Is to duplicate the replaced-clips sequences and use it as a station from where I pick up clips. By doing that you can always go back and use the same timeline-timecode to find your original audio.
I hope I made myself clear enough!