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all you have to do to render a dynamically-linked comp started with the "replace with After Effects composition" command is click on the "Render entire work area" command under Sequence.
Better yet, assign a keyboard shortcut to this invaluable command.
FWIW, mine is Alt + return.
To render a AE comp or anything that has a yellow or green bar you need to set the work area around it and goto Sequence>Render work area.

Hitting Enter Key only renders something with effects that make the bar completely red.
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