Since I upgraded to Yosemite on January 3rd, my Apple mail app is misbehaving. When I get new messages from gmail, they show up in the Unread and Today mail folders but not in the overall Inbox folder. After they are read, they disappear from Unread (of course) and are lost in the ether. If I search mail for a specific message, it finds it and indicates its either in an Important folder or simply in the inbox. Otherwise the message doesn't show up in Mail at all.
Also the mail remains on the gmail server when I access it directly on the web.
I've tried to synchronize the mail accounts but nothing changes.
I also turned on iCloud and iDrive at the same time.
Best Answer
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.