Outlook is downloading duplicate emails from a POP3 account

Outlook 2016 with a February 2016 update installed is downloading multiple messages. The recommendation is to revert to the previous build. See Outlook 2016 POP Account Problems for more information and instructions. (This is fixed in the March 2016 update.

Outlook users complain when Outlook downloads duplicate messages when they re-use Outlook data files. This is expected behavior when you use an old pst and leave mail on the server.

I moved my pst files to a new computer and set up Outlook to use the old pst files. When I try the first send/receive, Outlook downloads all of the emails off of the server even though I already have copies in the inbox. How do I get it to stop downloading the copies of the email? If I can't, how do I sort the email for the newly downloaded identical copies and delete them?

Duplicate remover utilities are available at Duplicate Remover Tools

You can't avoid Outlook downloading duplicates when you leave mail on the server. The "Mailbox Manager" file Outlook uses to keep track of messages that were downloaded is associated with the account that created it and downloaded the mail. When you create a new account, Outlook has to re-download all of the mail again.

There are ways to deal with this issue though:
1: Because POP3 only downloads mail that is in the Inbox, you can move the mail from the Inbox to another folder in your account online (log in using webmail) before taking Outlook online.

2: Let Outlook download the mail then add the Modified date field to the view, sort by it and delete all of the mail you just downloaded (that was previously downloaded.)

To delete the mail after it is downloaded, add the Modified date field to the view and delete the duplicate messages. (If you are leaving mail on the server intentionally, you may want to change the option to delete mail from the server when it's deleted from Outlook. Look in Account Settings, More Settings, Advanced tab.)

1. Close the Reading pane
2. Right click on the row of field names and choose Field Chooser
3. Select Date/Time fields from the drop down
4. Drag Modified to the row of field names and drop it between two fields.
5. Click on Modified to sort.
6. Select the first message you downloaded in the session
7. Scroll to the last (or last non-duplicate), hold Shift as you select the message
8. Press Delete.

If you have an ongoing issue with duplicate mail, you can use a rule to move older mail to another folder or delete it as it arrives. This method is usually better if you are creating a new profile or needed to remove the account and add it back to Outlook, but you need to set it up before you begin downloading mail.

1. Set Outlook to Work Offline (Send/Receive tab)
2. If you want to leave the old mail on the server, change the option to delete mail from the server when it's deleted from Outlook. Go to File, Account Settings, double click on the email account, click More Settings, Advanced tab.
3. Open Rules, Manage Rules & Alerts dialog.
4. Create a New Rule
5. Choose Apply rule on messages I receive then click Next.
6. Choose received in a specific date span
7. Click the underlined words and tick Before: [date]. Choose yesterday's date if you haven't downloaded mail yet today. Click Ok then Next.
   
8. On the actions page, select either move to the specified folder then select the folder or permanently delete it. Click Next.
9. Create any exceptions and click Next then Finish the rule.
10. On the Send/Receive tab, click the Work Offline button to go back online and let Outlook download mail.
11. If you moved mail to a folder, review it then permanently delete it before changing Outlook's settings for handling deleted mail in File, Account Settings, double click on the email account, click More Settings, Advanced tab.

3: Turn off any rules you use and move the contents of the Inbox to a temporary folder. Download mail and delete the old mail from the Inbox. If you use Outlook 2007 and up, you don't need to move your mail out of the Inbox; you can choose a different folder as the delivery location in Account Settings, select account > Change folder then create a new folder and set it as the default delivery location.

4: You could use "Duplicate Remover Tools" to remove the duplicated messages. But honestly, that's not necessary in most cases.