Wireless IgNition module -- it's where you actually put the key into there, it's also responsible for RF communications both with the chip key, and with the fobs.
There are two kinds of keys, regular blanks, and then the SKIM keys and fobs. The fob has a key blade inside it for backup unlocking of the doors, but it's the RFID chip portion that enables the truck for starting and driving. The blade will let you turn the truck on, and it may even get started, but after a few seconds it'll illuminate the red security light and shut the truck off and immobilize it. SKIM keys for these newer trucks have the upper portion that fits into the ignition. The (2010+? 2007+?) RKE fob has the blade inside the actual fob, so the only thing enabling the truck is actually the SKIM key, and thats the portion you stick into the ignition. I can't find a good picture and can't take one at the moment of my SKIM key. I don't have factory RKE so I've got two SKIM keys, and two non-SKIM keys. The non-SKIM keys will unlock and start the truck but will cause the immobilizer to turn on and shutdown/lockout the truck. non-SKIM keys look like a regular key, but SKIM keys have the part that fits the WIN. Even has a like, locking tab. And I bet you could use a hacksaw to cut the key blade off and it'd still work.
From what I understand the actual list of valid SKIM codes are all stored in the TIPM (IE the list of "valid" keys) -- and I think you only get 4, someone else might know that better than me though. If you've had new ones learned into the unit then you could've lost older ones, or, they could've done a wipe first so only the new keys were programmed. All of this is actually a lot more likely than the TIPM getting damaged by the trailer in such a way that it forgot JUST the SKIM key codes.
Try enough times with an invalid/bad key, and the truck will lockout, once in lockout even a valid key won't get it going, and it has to be reset, usually by a dealer.
There have been cases of a SKIM getting fried (very rare) and cases of the WIN/ECM/TIPM not communicating properly durign the shrot timeframe in which it has to read the SKIM. Some trucks you can cause the invalid key just by off/start/off a couple of times quickly. Normally unless it happens several times the truck won't lockout.
Could be they accidentally grabbed one of their unchipped/non SKIM keys to start the truck with...?