One last update on this one..

Once we were airborne on our first flight, I saw our flight to JFK was scheduled to get in about 15mins early. Messaged @Delta on Twitter and they were able to get us on the flight and get us assigned seats. They did say that they "couldn't reissue the ticket because the flight was under airport control" (despite it being 5+ hours prior to departure).

They emailed me my confirmation, which had the flights and seats in it. But that segment disappeared from the app and delta.com

Anyways, after the worlds longest jitney ride (had a stop, and the bus driver took nearly 10 minutes at the first stop), we got to the gate precisely 20mins prior to departure.

Scanning our BPs made the scanner go red; when I told the GA which seats were ours, he indicated they had given them away/upgraded passengers because we weren't checked in. The GA mumbled, asked someone to pull those UG'd pax back to their original Y seats, re-printed our BPs and let us board. Said all the problems could have been avoided if the agent that got us on the flight had just checked us in!

Feel bad for the upgraded pax that we displaced, but we are onboard and headed home, so all worked out I suppose.

(and no, our bags didn't make it according to the bag tracker. They likely would have if we were confirmed on the earlier fights prior to checking them in so they could be tagged HOT, etc. no worries there though; expected they wouldn't make it)