I didn't read all your note carefully.
In your previous Encore project for DVD 1 (or whatever), right click on the "asset" for the timeline (the asset for a dynamic link is the Premiere sequece, not the Encore timeline that was created), and pick "revert to original." It should pick up your changes from Premiere.
Note that to update markers, you must select the video in the Encore timeline itself, right click, "update markers from source." You will lose all previous markers. If you created the markers in Encore, you must update manually.