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Engines don't mind a fair amount of water getting sucked in if they're running and warmed up. If the water clogs up the air filter, that's obviously a problem, but I have to wonder if the filter was dirty at the time, making it worse than it normally would have been. Is it a stock foam filter?
Hydrolock happens when the engine is not running and enough liquid gets into the combustion chamber to nearly or completely fill it when the piston is at the top. It won't happen to a running engine unless the engine goes underwater.
Do you think the problem could have been that the spark plug wires got wet and were arcing to ground somewhere, making you lose spark intermittently on one cylinder? That's a lot more common than a little water in the intake causing power loss.
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