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Yeah, Im dual US/Swedish citizen, and the check in is isolated each time. I present my US passport when going to the US and my Swedish Passport when going to the EU. No biggie and never had any trouble throughout my life.

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So in the Schengen logs, it seems like you keep entering Sweden (or wherever you transit) but never leave it?

Or do you show your Swedish passport on leaving Schengen?

Not OP, but in my experience they will look for a Schengen entry stamp during the exit control.

Showing e.g. a Swedish passport for border entry and exit, and a US passport for check-in works fine.

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