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It sounds like you've put it in the frame bag numerous times (25- 50 rides?) and never had problems?
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No, I haven't done it that many times, I just don't see how it could be harmed by it. The water filter is light and mechanically very simple, with no hard and heavy parts bouncing around or rubbing against each other. I always try to pack my frame bag so that the contents does not move very much, though, using clothing items if necessary to pad things, and this far haven't had any problems.