If you put your bike down in water it is always a good idea to dump the oil at the earliest opportunity, no matter whether you think its gone in or not. It's not just the water that's the problem, a small amount will evaporate and exit through the crankcase breather. The trouble is river and standing water will have silt, sand and god knows what else in it, which ain't going to be good for your motor. In the top end this debris is not so bad as most of it will find its way out fairly quickly, in the crankcase it will be trapped, until you do something about it manually.

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