summer14, In case you haven't resolved this yet.
polzbert's solustion is excellent, assuming you have a backup drive using Time Machine. However, did you try rebuilding the inbox? If not, here's how:
Select the mail box that's giving you trouble in the left pane of Apple Mail. Then choose "rebuild" iunder the Mailbox Menu Item. This has resolved countless mailbox glitches for me in the past.
I tried similar solutions to no effect with an identical problem. I then did a full restore from Time Machine of my entire system back a few days to before this problem. Guess what? Problem was still there. Crazy! My iPhone 4 and iPad 2 retrieved my email fine. I used Get Info in the Mac mailbox that did not display. I saw there was a message from an "unknown user." I used the web interface on my email and I deleted a block of messages including that one. I started Mail up and it immediately began to work again. There appears to be some way that an email can be corrupted on the server and cause this problem on Mac Mail although not on the IOS devices. Anyway, if all else fails, try to see if you have a corrupted email message on your server.
I had this problem and it was fixed with a call to Apple this way (which resets the Mail app and forces it to reload all data):
Double click on home button at bottom of ipad screen - this brings up a bar of apps at the bottom
Press Mail ap until it start to jiggle
Press cross on this ap to delete it
Press Home button again to go back to normal home screen and press Mail again
For me, that fixed the problem
Hi there - can someone please tell me if i am to take the advice from this page (which looks great!) to fix up the disappearing mail... when i am asked to open a mac account again do i lose my existing emails?? it seems like i am starting up fresh again and i am scared to lose all of my work to date
Please let me know if anyone has an idea of this