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I thought airlines still had to file passenger manifests with CBP separately, no?
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Yes, though that's separate from the flight plan.

There's also several different ways to transmit the passenger manifest to CBP - including over a CBP-provided VPN and IATA "Type B" messages sent through ARINC/SITA.

The network for Type B messages is also independent of the Internet (it was developed 60 years ago).

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