Is there a way to copy the Encore Chapter marks from a nested sequence into the main sequence that they get exported? Or is there an easy way to at least jump directly to these marks of the nested sequence in the main sequence?
No to both. Sequence or Encore markers turn into Clip markers when a sequence is nested. There used to be a way to navigate directly to a clip marker within the sequence, but inexplicably Adobe removed that incredibly useful abaility for CS6. Please let them you you want "clip marker navigation within the sequence" back.