Just an update (thanks oliver2002, you were absolutely right), wife made it fine to AMD. The customs etc was in AMD.

The Jet Blue folks checked in the bags all the way to AMD from CLT. She also gave up her carry on at the gate in CLT all the way to AMD.

Now. The problem. That carry on did not make it. 4 other folks did not get their bags either. 2 did not get their gate checked carry ons and one did not get their checked in luggage. Took her 2 hours to get the papers filled out. But, at the least she made all her connections sans the bags all the way.

Turns out, my dad had flown the same route 4 or so years back. CLT-JFK-DEL-AMD and remembers all customs being done at AMD both ways.

Hopefully wife gets her carry on bag by tomorrow like they promised as all her clothes were in the carry on.