Did you accidentally download your Yahoo Mail emails to your computer?
To copy the email on your computer back to the Yahoo servers:
Update the existing POP3 configuration to "leave mail on the server".
Next, add an IMAP configuration for your Yahoo Mail account to your mail program:
http://www.emailquestions.com/yahoo-mail/7237-setup-imap-connection-yahoo-mail.html
Copy the email from your POP3 inbox to the IMAP profile inbox.
After you have verified that your mail is viewable in the Yahoo Mail web site it should be safe to remove the POP3 configuration from your mail program.
To copy the email on your computer back to the Yahoo servers:
Update the existing POP3 configuration to "leave mail on the server".
Next, add an IMAP configuration for your Yahoo Mail account to your mail program:
http://www.emailquestions.com/yahoo-mail/7237-setup-imap-connection-yahoo-mail.html
Copy the email from your POP3 inbox to the IMAP profile inbox.
After you have verified that your mail is viewable in the Yahoo Mail web site it should be safe to remove the POP3 configuration from your mail program.