You have two options as I see it, in Encore.

you can export the entire lot as one movire from PPro and then build a single timeline in Encore and have buttons to jump in a various chapter numbers and achiever your goal that way. the problem with this is that in Encore 1.5 you cannot jump out of a timeline at the end of a chapter so it will flow straight into your second clip.

Alternatively, and you best approach I think, is to export two seperate timelines from PPro. The build two timeloines in Encore and have a button plat each one. You can also create a third button as a play-all if you want. This way you get full control.

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