If it were me, I would ask them to explore the possibility of cleaning up the existing caulk, and treating the whole thing with "Eternabond"; right over top the old caulk. It would be a LOT less labor (it's hard and very tedious to remove all that old caulk without destroying the roof), but more expensive in materials, and the repair would basically be permanent.
If the roof membrane is in good shape, this could be a much better alternative, and may even be cheaper.
2014 Jay Flight 28 BHBE
2015 RAM 2500 6.4L HEMI, Tradesman 4x4, 3.73
Blue Ox SwayPro (BXW 1503)
Upgraded from an REI internal frame backpack and a Eureka 1/2 dome tent!