There are about 3500 bees to the pound, so they say.
 
Bees are remarkable at being able to withstand wet weather.  They cluster
up so that the rain washes away; hopefully not too many got blown around.
They should dry out o.k. especially as you've given them some space for air
and made sure they won't lose their roof again.  The conditions might set
them back a few days, but they are likely to survive fine.
 
I've found colonies in the spring after cold wet wind storms where the
covers are off, smashed in the trees several feet away and the bees
hunkered down in a tight cluster.  I covered them back up and to my suprise
they seemed no worse off a week later.