I suspect my company swapped engines. Is it possible?

All I have to say is WOW.
It would be hard, almost impossible to swap the engine and not be easily detectable.
Does the mileage on your ecm match the truck?

 

odds are somebody used your truck unless you own it outright! even if it's a lease purchase they can put anybody in that if they want. if somebody's truck was in the shop and they needed to use it odds are they probably let somebody use it said here use this this guy's gone go deliver your load so who the heck knows that's probably what happened I don't think there was any kind of an engine swap at all..
I would check the ECM miles versus The hub miles what were the miles when you parked it does it look like there's added miles out to the odometer ?Bottom line is unless you possess the title "even if it's a lease purchase truck" they hold the lien they can let anybody drive it if they want to if it sits for more than a week probably what happened there chief

 

The D13 doesn't have a plate with the serial number on it?

 

That wouldn't be the first time something like that happened.
I once worked for a company that had one of their engines get ragged. The owner bought a new truck on credit then swapped the engines and let the new truck be repossessed.
Seems with the newer truck it would be easy to know since everything is computerized.
@Ridgeline probably knows how to figure this out.

 

It's possible. But a straight swap? You would know it the minute you started her.

Other drivers in it? Certainly. Always comes back with a problem. My last one had it for three days and turned a perfect truck condition in terms of shop needs from 100% into a list of problems needing two days TLC in a shop.

 

I have a Cummins and its located on the drivers side. I would be surprised if a D13 didn't have something similar... Heres an example of Cummins