The entire thread is gone, or just a comment?
If someone posts a comment on an old thread, that thread gets moved to the top of the queue. If that last (recent) comment is deleted for whatever reason, the thread itself returns to the list according to the date on the previous most recent post. It hasn't disappeared, it just went to page 2, 3, or wherever it would happen to fall. This is most common when spammers revive years-old threads and we delete the spammers comments (and lock their account).
PM sent with further info.