Searching around on the net I stumbled upon the helpful powershell command Clean-MailboxDatabase. According to the MS documentation on the command, running this against your mailbox database will scan for disconnected mailboxes that have not yet been marked as disconnected in the Store, and mark them as such.
After doing this, my boss' mailbox showed up in the disconnected mailboxes pane in EMC, and I was able to reconnect it using the Connect-Mailbox command. Crisis averted, everything went back to how it should be.
I should note that I have still not been able to determine what caused the mailbox to disappear in the first place, but should this happen to anyone else hopefully this will do the trick for you.
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