I have recorded a live drummer with a backing song, and mixed down to left right stereo, at the time of recording we also recorded the video and imported into the project loosing the camera audio, after a bit of editing and shifting around the video and audio synced perfectly and sounded and looked great but then it all started to go horribly wrong.
After trying many attempts to export both tracks audio video I would only end up with audio in whatever format I chose
this got me so wound up that I actually had an attack of DAW RAGE, I have come to the conclusion that it can’t be done or I am missing a fundamental process somewhere or maybe a later version fix, if anyone can throw some light on this I will be most greatfull.
Try
File > Replace Audio in Video File
then choose your files …