How can I recover my email?

the function of rebuilding your mail on the mac mail is not to restore lost emails but to restore lost or damaged content in exiting email

Mail (El Capitan): Rebuild mailboxes

your deleted messages may still be in the local deleted folder (in your mail app) or the mail server your mail domain is using.

If not then If you have a time machine backup you can restore deleted emails using time machine

http://pondini.org/TM/FAQ.html

Try re-indexing the mailboxes. This can take awhile if you have a lot of mail.

Reindex messages For El Capitan, try looking in V3.

Reindex messages (2) See post by Linc Davis

Is this an IMAP or POP account?

Check in your User's Library/Mail folder. Do you see a V2 folder? If yes, it should be empty except for Mail Data folder. Do you see other folders?