Ain't found nuffin on bats, mate, but this one on nouns of congregation for birds is wuite interesting

http://www.southendrspb.co.uk/nouns.htm


This one has bats in it:

http://www.angelfire.com/fl/JackCraig/ANIMAL.html

but they only suggest "colony", which, to me, suggests them when they are roosting in their caves, rather than when flying.

How about "a swarm"?