I've had my 6006's on timers before. No problems other than the occasional snail that decides to crawl inside while the stream is off. Tunze says that the on/off cycle should not be less than 1 hour or you will cause damage.
As bowfront said, the main problem is pureeing a fish or braking the prop because a snail goes in it, in this case the damage would not be covered under warranty.
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