I think when the waitlist clears, an agent has to resolve the issue.

In a case such as yours, where it's obvious what you want to do (replace a connection with a non-stop), they would clear it, reissue, and send the email.

In a situation where it may not be as clear (e.g., you're waitlisting to a different city), they would call in case they have to make other changes at the time time, or if the taxes changed and they needed to charge you.

I have a feeling you checked the itin when it was cleared but not yet resolved. I doubt you had any risk of losing the space, and had you not noticed this, you would have received the email in a few days.