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I opened Apple Mail, it said it couldn't create a sent messages folder on the server and that it created its own locally. Then I logged into me.com and saw that all of my sent messages were gone.
 
Are you saying that there's no default Sent folder on me.com?

No. I'm saying that all the sent messages in the sent folder disappeared.

I have them backed up on my computer. Is there any way I can put them back in sent folder on the server?
 
Go into Time Machine, select all sent messages, restore. Once restored in Mail.app, they should re-appear in Sent folder on me.com.
 
Time Machine didn't recognized any backups for Mail, so I dug into the backup and found the sentmessages.imapmbox, had to find some complicated instructions to import it into Mail, then I dragged all the messages back into the sent messages folder.

All is well.
 
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