We have integrated our Segment instance to Marketo, but the Marketo V2 sync did the exact same thing...duplicates. We worked with one of their solutions architects to create a Custom Function. This passes data from the track event tied to an email address (we were missing email before). The Custom Function also lets us write to our Custom Objects (Marketo V2 only updates Custom Activities) which means our teams can take advantage of Velocity Scripting.
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