And I'm going to be PISSED if they charge any penalties or fees for something they obviously didn't take into account and is totally their fault.
We'll see what happens.
Okay! That was a LOT less painful than expected. Expedia was cool with dealing with it. As soon as the rep saw the itinerary, he paused and said "Oooh, yeah. Hmm. That's not right. Let me call Delta for you, see if we can get that fixed." He put me on hold for about five minutes and came back with a new flight schedule. It's an hour earlier and the stopover is at JFK and not Atlanta, but it makes a lot more sense! :)
And to be safe, I called Delta just to check everything with them, they said everything looks good, their change-of-itinerary email was just a mandatory thing, and it's all set. With NO FEES OR PENALTIES.
YAY! :D