Boy...a complete rebuild of the top and one side of your trailer due to structural issues? Hopefully you are still within your warranty period?
I'm not sure about what to do, but it sounds like step 1 would be to get a write up of exactly what all the shop is going to do and have the costs of all the repairs itemized. Then you can compare the repair cost to what you paid and hopefully simply tell them you want a different trailer because yours is totalled.
I'm pretty sure the manufacturer will object to that, at which point I'd go see a lawyer and find out what you should do.
NOTE: I dunno exactly what is going on with the roof, but is it as simple as pulling back the rubber roof and reattaching some of the plywood sheeting to the vehicle's frame? If so, that seems to be quite a ways from a complete rebuild.
Is the shop a Rage'n dealer? If not, I can imagine issues will arise.
