Rest assured your MIT email is still there, but is simply hidden from view. The default Evolution settings cause it to display your local mail folders, rather than the folders on the email server.
Unfortunately, Evolution's default settings cause it to open in a very small window, like this:
You should make the window larger, by dragging the bottom right corner of the window, or by clicking the "Maximize" button at the top right corner of the window.
Once the window is large enough, you should be able to see the folder list at the left. If you view the entire folder list, it should look like this:
Find the entry called "MIT mail" and click the triangle on the left hand side. You should then see "Inbox" below "MIT mail". There may be a triangle next to "Inbox", which you can click to display all your folders on the IMAP server.
The correctly configured Evolution window should look like this:
(click for larger version)
You will only need to make this change once.