>> Here is my problem.  Should I extract the honey in the upper BC in all 3
>>hives
>> and leave the partially filled and capped frames of the honey supers for them
>> over the winter?
>
>No, I wouln't.  Never (almost never) extract brood chambers.
>Everything in the bottom two boxes is theirs.  Everything above is
>yours.  Trust them to decide how much to give you.  Sometimes you
>might have to remove a few combs to 'loosen them up', but save them
>and put them in again later.
 
I am in the same area as the original poster (SF, Calif.), and have had
what appears to be a varroa related change in bee behavior. I also run
doubles, but almost all of my hives have filled the second story completely
full of honey in spite of ample supering. They never did this before the
mites got here. As a result it has become quite time consuming and rather
hit or miss treating for varroa. I have had quite a few hives which did not
get the strips into the brood and as a result died or had to be retreated
in a weakened state. All of the big commercial beekeepers that I talked to
at the CA state convention are using single story brood chambers, and claim
not to notice any reduction in yields in Calif. I have therefore decided to
go to single stories and have inserted the excluders after chasing the
queens down. To the original poster I would recommend extracting the honey
in the second story and using a single story brood chamber from now on. Two
brood chambers don't seem to provide any advantage in this area to be worth
the extra hassle.
 
> To my surprise,  The bees have moved down into the lower BC in all
>> hives and filled and capped every frame in the upper BC and left the suppers
>> above alone.
 
This is not a good sign. With the warm weather we have had and the
eucalyptus flow that you have noted your bees should be strong and working
in the supers. All of mine that were successfully treated with the strips
are now doing so. Your bees' behavior sound suspiciously like what happened
to some of my bees that did not get the strips into the brood because of
too much honey in the second brood chamber. You may need to insert strips
into the lower brood chamber right away if this is the case. Good luck.
 
Mark Jensen-Double J Apiaries           [log in to unmask]
Los Altos Hills, CA, USA                     fax 415 941 3488