I'm reading "Fool Moon" by Jim Butcher right now and I thought of this question. Someone asks Dresden if the fact it's cloudy and raining will affect the werewolf cycle. Dresden replies that, while we might not be able to SEE the moon, the magic used to create a werewolf is still there regardless. So an eclipse of the moon, like the clouds, wouldn't affect a werewolf.
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According to Harry Dresden, anyway. ;-D