When you say "reconnect" do you mean "link"? In this case... If I understand you correctly, then you need to unlink your audio from your video (option-L) then select your new audio and video, and hit option-L again. when you unlink, you will see that your video clip will lose the underline underneath the file name. Once you re-link, the line will re-appear.
This will link them in FCP, but it won't replace the original audio in the original video mov. To do this, you'd have to export a movie from FCP.
Nah, what im trying to do is reconnect a mov to an existing fcp project, but as Dolby E cannot be edited (other than straight cuts) i want to connect tracks 1&2 to tracks 3&4 now. Originally the stereo tracks were on tracks 1&2, but now Dolby E sits in them tracks.
I can always get them re-ingested with the audio swapped, but trying to avoid that.