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I replaced the old acrylic pilothouse windows on my boat with polycarbonate, because it is stronger (I think this is because it flexes more to take a load than acrylic does, so scratches easier but avoids breaking better).
I actually replaced the windows twice, because I made the mistake of putting RainX (designed for car windshields to cause rain to wash off quicker) on the new windows. This destroyed the UV coating (polycarbonate slowly goes cloudy when UV damaged), and within a few years I replaced the windows again. So don't ever do that :)
I've used neoprene gaskets to seal the windows, and they worked well. I've also used polyurethane adhesive sealants, whatever was available at the time, a Sikaflex, LePage's Quad, Wang Xin [I got that in Chile from a automobile glass shop--it was the only thing available that would set at temperatures below 10C] and a Brazilian one. All the polyurethane adhesive sealants that I used worked well.
If your windows are bolted on, as opposed to glued into a frame, it's important that the holes drilled in the polycarbonate need to be at least twice the diameter of the bolts, otherwise different expansion rates will result in cracks around the bolts after several weeks.
It occurs to me that if you have the type of windows that go into an extruded aluminum frame, held on both sides by a little lip, it is possible that they are designed for the stiffness of acrylic.
If you're buying from a non-marine supplier, you'll want to confirm that the polycarbonate they sell has a UV coating on it.