If the weather does not change for a long period of time you could use Control N to reset it. This will produce some strange effects, like sunshine and rain, but it goes back to normal shortly. The best method is to use control N, save the game, exit to the main menu. and reload. The game restarts with calm seas and clear skies.
I first used this to help me complete a photo mission to Hiroshima. Although the Bible says it will never happen again, the game's engine gave me an intense storm for 40 days and nights.
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