The question is really if the emails that disappeared are still present on the computer.
I went to ~library/Mail. Then found the POP folders where the emails have been saved to the computer. Once that is opened. It showed “Deleted messages, Drafts, Inbox, Jun, and Sent messages” this may differ from user to user. However, I clicked on “Inbox” and all my messages were there under “messages”. I could open them and read them.

Therefore, the files are not lost.

To repair:
1. Quit and reopen Mail
2. File Import Mailboxes. Select Apple Mail and continue
3. Find the “INBOX” file. ~Library/Mail/POP…./Messages/Inbox
4. Do not open the inbox, select it then press “Choose”
5. Those messages will now be in your MacMail Under the “ON MY MAC” heading on the left hand pannel.
6. under “ON MY MAIL,” there will be a folder titled “Import” and the “Inbox” folder is there.
7. select all the messages from the imported inbox. Right click. Select “Move to” and select “Inbox” .. Your inbox.
8. Repeat steps 2-7 for “sent messages” and move imported sent messages to Your Sent messages.

If the messages are no where to be found on your computer, then the files are likely not there, and you will need to restore some files.

https://discussions.apple.com/thread/2364054?tstart=0