>>I am in SC, and for the first time was beekeeping this summer.

Gavin has provided some very good advice so I won't repeat it. :)

>>I looked inside at that point and it would appear the queen had 
died for I saw very little brood.

This should not be the logical conclusion.  Especially in feral 
colonies, bees make provisions for a new queen before the old one 
dies.

The bees could have swarmed leaving behind little brood and a virgin 
queen.  Did you rule this out?  If there are some bees with the 
little brood you did see, I would meticuously check for a virgin 
queen.  Keep in mind, virgins are not easy to spot.

>>...this week, it appeared business as usual in the hive.  But then 
yesterday I noticed no bees at all, and they are gone.

The bees could have absconded in both cases.  Were the hives in 
direct sun light?  If you provided no top ventilation and don't use 
screened bottom boards, the colonies could have been stressed out by 
overheating and decided to look for cooler quarters.  Do you think 
this is possible?

>>My question is on how to clean the frames and boxes.  Do I just 
toss out the foundation and all and order new?

Why do you feel you must clean the hives/frames?  Unless you find 
positive evidence of disease or infection, you can just re-stock the 
hives with new bees.

Waldemar

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