(1) - Mail questions go in the Software forum
(2) - You probably had some sort of preferences glitch.
Try quitting mail and relaunching it. If you mail doesn't appear, you may want to do a restart at some point.
Your mail is not in some invisible file anywhere, it's in a folder in ~/Library/Mail where "~" is your home folder. You can always make a backup of that.
Without more details of what you've tried etc. I'm afaid I can't be much more help.
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