There is a process for getting them even again. Basically it involves raising or lowering the bunk all of the way and holding the button until you hear the motors whine a bit and then stop. Then release the button. This resyncs the motors. Obviously, if one side won't go down at all, that is a different issue that may require a bit more work.
If you do a search for "front bunk uneven" you will find a lot of info on what has been done by other owners to fix the situation.
2016 Thor Hurricane 35C with pups Piper and Annabelle
2013 Ford Fiesta toad
FMCA - F457085
Blog - https://traversity.us
I had the same problem, do as jpmihalk suggested. On mine, I had to cycle through several times. Each time going all the way up until the motor stopped and all the way down until the motor stopped. I actually waited a few seconds after I no longer hear the motor until releasing the switch.
This post is opinion based on experience.
2015 Hurricane 27K
2013 Sea Ray 220SD
You can sync the motors the same way you would sync a slide. Push it all the way up or drop it all the way down.
We also sync level it using the pins as well, but I don't amp out the motors that way. While we are traveling, we set the bed down on top of the pins right after we push it all the way up. The mattress is a bit thicker than the clearance which pushes the bed back down a bit after it is flat against the ceiling.
Just one word of warning, moving the bed up and down crooked too often will rub the wall paper off the wall.