Select the asset in Encore (not the timeline, but the original files you imported), and use "replace asset." Make the name of the new export from PR different. Replace the video and audio separately if you (as preferred) used demuxed assets.
If do not know what happens to the markers in this scenario. But I assume they do not update. I hope that they update when you right click the timkeline and pick "Update Markers from Source." I was always doing this with a dynamic link, but it does not say that is the only source it will "look" at.
But it is possible that it will foul up chapter links.
Let us know.
The "replace asset" function you pointed me to worked perfectly. Even though the audio didnt' change, I replaced both the audio and video and the original timeline updated perfectly with the new material.
Thank you very much. I wasn't aware of this feature and your tip got me back on track in just a few seconds without having to start over!