So in case this happens to anyone else, here's how this seems to go:
Don't waste your time contacting Fedex, they're useless.
Contact Apple, they'll look into it, hopefully you don't end up like me where after carefully explaining what happened, they think your trade in kit got lost on its way to you instead of on its way back to them.
Once Apple realizes Fedex has lost your old iPhone, they'll initiate a refund request and file a claim with Fedex
This next part hasn't happened yet, but I've been told once everything is done with the Fedex claim, Apple, will forward it to Citizens One and close out your loan.
I have been getting daily email reminders I have X days left to send in my old iPhone, which I'm told is just automated and I have nothing to worry about.
I'm going with the theory that some Fedex worker in Keasby, NJ knows what all these identical packages going back to Apple are and decided to snag mine. But who knows.