Hansel,
http://www.keystonerv.org/forums/sho...ight=insurance
This link is the account of our roof damage in June 2013. They replaced all the skylights, refrigerator vent, roof vents, A/C shroud, tank vent covers, EPDM membrane, some molding, all of the A/C ducting from the A/C toward the rear of the trailer and a small bit forward of it, the majority of the 3/8" OSB decking and several of the roof trusses. The total estimate was $8700, but the final cost came in slightly over that. The trailer was a 28' Springdale fifth wheel.
I'm sure there's some inflation as well as some differences in work to be done, but $12000 seems a bit steep. You might want to get another estimate just to be sure. But, yes, it's not cheap to replace an RV roof. almost all of the cost is in labor, materials really aren't that much of the total charge.
Good Luck