Once you have turned them off in a game (click on them and uncheck the box...), how do you turn them back on? 
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Something related, is there any way to see old messages? Sometimes I close them too quicly
You can look in the box at the bottom and scroll up to get specifics (ie what date a decision fired etc...) but not recall the message popups.
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It's best to turn on log for all the messages, but most times they are not as detailed as the popup (casualties and losses are not shown in log)