All Email in inbox is deleted when trash is emptied!

We were cleaning out our inbox and when the trash was emptied, the trash was wiped out and all emails remaining in the inbox. Where did they go? how do we get them back? What does it mean when the message says "indexing messages" when trash is emptied? Please help. Thanks.

Proceed as follows:
1. Quit Mail.
2. In the Finder, go to ~/Library/Mail/POP-username@mailserver/.
3. Locate INBOX.mbox and move it to the Desktop.
4. Open Mail. A new empty INBOX.mbox will automatically be created within the account folder.
This will allow you to continue using Mail normally while trying to solve the problem of bringing the messages back into Mail.
If you ctrl-click on the INBOX.mbox package and choose Show Package Contents, you'll see several files there. mbox is the most important, as it is where the messages themselves are stored. You may also see an Incoming_Mail file that, if present, may contain additional messages.
Both mbox and Incoming_Mail are standard mbox files that you should be able to import back into Mail doing File > Import Mailboxes and choosing Other / Standard mbox as the data format. Problem is, the mbox file is probably too big for Mail to be able to handle it.
You may solve the problem with a third party utility, such as Emailchemy, that breaks mbox into smaller files that Mail can import afterwards.
Note: For those not familiarized with the ~/ notation, it refers to the user's home folder, i.e. ~/Library is the Library folder within the user's home folder.

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