Cladding removed from sides of dormer, should it be covered if not being replaced for a week?
I would cover the openings with plastic sheet or some other water proof material. It doesn't have to be perfect, just enough to prevent the rain getting onto sensitive surfaces. The timbers should be treated and should be able to withstand some rain, but you don't want water getting into the walls etc.

The main issue I see would be how to ensure it was properly secured, but there should be enough exposed timbers for you to staple into to get a good enough seal.