Part of that brainwallet hacking "brainflayer" which was released had some bloomfilter stuff to check large amounts of keys at once
https://github.com/ryancdotorg/brainflayer. I don't know if it's something you can repurpose for whatever you're doing. See that "hex2blf" script.
In any case, if you only need to check thousands, why not just write a loop to look them up one at a time. This could be problematically slow if you actually want to check hundreds of millions, but I would think that thousands would be trivially quick on a modern computer.
Thanks, I'll take a look. I'm looking to check 100k addresses.
Found this before posting, it's good for a small amount, but checking more than 1000 it prints "Error" instead of the balance.