Interesting question. I've not tried that and would have to go look at my trailer to see if there could be a problem. But, from memory, doesn't the bunk attach to the top half of the trailer, but when it's down, don't the legs go into holes in the lower half? If so, I imagine there could be some rather bad interaction on the various parts of the bunk as you lowered the top.
However, if you left the legs up, along the sides to the bunk as it would be in the stowed position, then I think it would be attached only to the top half. It might lower safely and not be damaged this way.
Study your bunk carefully and see if the top can be lowered without unhappy interactions when it's down. Once down, if you determine it's safe to do that, look at it to judge how it will ride under the stresses of travel on the road.
Hi-Lo 1707T - Tire Minder TPMS on Tow Vehicle and Trailer, 300W Solar Battery Charger, Equal-i-zer WDH
2014 F150 Platinum 4x4 3.5L EcoBoost SCrew