Not sure I'm answering your question but the nest will always reference to the original media. If you import the master timeline to AE it will make the nests subcomps with the correct media etc.
Why would you want to use final cut?
There is no one click option for this, but you can always remove the nested sequence, and then copy/paste the original clips into the empty space.
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So far, I think the best work-around is contained here, where you use the Shift-T option to identify the in and out points of the original media.
I suppose this section is the key to replacing the nested elements:
Reveal a source frame from a nested sequence
If you want to reveal a clip in a nested sequence (for example, to edit it), you can quickly open the source sequence at the exact frame you want to reveal.
- 1.In the Timeline panel, target the track in which a nested sequence is located by clicking the header of that track. If you target multiple tracks, the targeted track that is on top is used to select the nested sequence.
- 2.Drag the current-time indicator to the frame of the nested sequence that you want to reveal in its original sequence.
- 3.Press Shift+T to open the source sequence in the Timeline panel, with the current-time indicator at the frame you specified in the nested sequence.
- 4.Double-click the clip where the current-time indicator rests to open the clip in the Source Monitor.
I have found it to be a good practice to make a duplicate of a sequence before nesting tracks.
This makes reverting to the original tracks a much simpler operation if required.