Inbox messages not visible after upgrading to Yosemite
Your messages are not gone.  

Apple Mail is not displaying the Exchange or G-mail inbox properly.  

I tested this with 2 systems: 1 on Mavericks and 1 on Yosemite.  

The Mavericks mail worked correctly and the Yosemite would stop displaying the inbox.  I was able to perform operations (read, flag, delete, move) messages on the Mavericks system and the actions would correctly show on the Yosemite system once I re-synced the mail application.  

Furthermore, I only needed to click on my iCloud-based account and then go back to my Exchange account for the inbox to be displayed properly.  However, after about 30-45 seconds it would again stop displaying.

This looks like an Apple bug.

I hope this helps and that Apple can fix this annoying bug soon.