you say the new version has teh same TC?
then shouldn't you be able to simply control click on the clip and "Batch Capture"
the old media will be deleted in favour of the new,
and the markers will al stay in place.
alternatively,
make the original media offline, and re-capture.
for safety, you can keep the old clips, too.
copy the marked clips into a new project.
make them offline but keep them on the disk
recapture.
the new captures will go to a new capture scratch folder as you are now capturing in a new project.
nick