Well, knee injuries are the foundation of the orthopedic medicine business, so don't just assume that you will be ok if others are.
Repetitive stress injuries can be be quite serious. Take the bike fitters advice and learn to ride your bike with the proper fit. It will take some getting used to, but your knees are worth it.
If you don't like the high center of gravity on your hybrid, you can consider a road bike or various other newer designs that lower your center of gravity. You definitely trade comfort for stability with some bikes.
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