This is an information post, designed to make some information available to myself and others. I did NOT discover this but I thought it was something pretty important.
When disabling an Exchange 2007 mailbox, it sometimes will not automatically show up in the "Recipient Configuration | Disconnected Mailbox" bucket. It takes running the command:
clean-mailboxdatabase <mailbox database>
Once that command is run, you can reconnect it or do whatever you need to it. Thanks Missy and Amit (If you want the full explanation and pictures, click here)!