It sounds like the rebuild failed in spectacular fashion. Was there anything in particular you were trying to accomplish when you attempted it?
Given the symptoms, it sounds a lot like Mail HAS your emails, but one or more are corrupt (likely just one) - the system it uses to display your message list is falling over when it spots them in the database, and so it doesn't show you any messages at all.
How easy this will be to fix is likely to depend on how many email accounts you've got set up, which of these are POP/IMAP based, and whether you had additional emails stored in the On My Mac folders section of the Mail sidebar.
Of course, if you have an up-to-date Time Machine backup of just before the problem, things may be quite simple... If you have no such backups, I recommend starting out by making one.