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Sorry, but the answer isn't very satisfying:
It appears that the "first" instance is the one that is kept, where "first" refers to the first instance encountered as After Effects walks the compositions doing a search. Unfortunately, the algorithm for that search is not one that is easily/usefully explained. As Dan Wilk said, "It's deterministic, but not designed... It keeps one of them. That's about all you can say."
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