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I have to eat crow - my restriction of no null or duplicate values in the ID column was insufficient, so a small number (~10) snuck in and that appears to be responsible for this behavior. Removing those duplicates results in the number of rows output by pregel matching the number of rows in the vertices DF.

Sorry to waste everyone's time, glad to see it's a me issue and not a software issue at least.

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@SauronShepherd
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@confusedamazonian
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@SauronShepherd
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@SemyonSinchenko
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@confusedamazonian
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