I managed to get my bunk "out of sync" by not running it all the way when lowering and raising it. One of my pins was jammed. I was able to release the pin by pushing up and/or pulling down on the bunk while someone else pulled on the pin. Not easy to do, took a lot of effort.
Once the pins were out I was unable to move the bunk as it was obviously not level and the controller (located in cabinet above driver's seat)would shut down each time I tried. I eventually unplugged one of the motor controllers and tried again. The controller would operate for a inch or so of movement then shut down. I would turn off the controller and then turn it back on and move an inch or so at a time. Eventually got the bunk all the way up on both sides. Was then able to run it all the way down and hold until motors synced. Seems to cycle correctly now. Pins go in and out easily now.
Mine is in a 2016 Thor Miramar.
1998 Min Winnie, 2000 Winbago Journey, 2015 ACE 29.3
2016 Thor Miramar 34.2