Hate to say it but from past experience of what others have reported it probably has done your batteries in. You may be able to get them back again but they will most likely not be at the same new performance before they was discharged below the 50% charge state.
I have never returned any of my trailers back for warranty work but if I did I would most definitely remove my large expensive battery bank and let them deal without a 12VDC battery source. I might connect up a Lawn Mower 12VDC battery to get me to the dealership and be legal with DOT safety regulations.
We have alot of money invested in our battery banks and you know the dealership is not going to replace them if they were discharged during the time the trailers set in their shop.
Just my thoughts here
Roy Ken