Duplicate emails are an issue with POP accounts. POP was meant to be downloaded then deleted from the server, but many users select to "leave on server". Each message has an ID assigned on the server. When Outlook downloads it checks the IDs to see what it has and what needs to be downloaded.
If a server updates their software or reboots the server, all messages left on the server is given a new ID. When Outlook checks it sees all new IDs and download all the messages left on the server.
If Outlook get corrupted it can loose IDs and download again.
Your best option is to move to IMAP if possible.
If you want to save older messages on the server, in your browser, move the messages out of the Inbox to a folder you create. Email clients only download Inbox messages for POP accounts. If you ever need to download again, you move the messages back to the Inbox.
You can download this script to remove duplicates.
http://www.scriptsformac.com/wp-content/uploads/2012/07/Remove_Duplicates_v2.1.z ip
- To install, click on the Script icon (squiggly S to the right of Help) and select "About this menu".
- Click on the Open Folder button to open the Script Menu Items folder in Application Support.
- Put the script in this folder.
- Select the script from the Menu bar to run.
Best run on fewer than 1000 messages per folder.