This is just a quick post detailing a neat feature of Mail and the ability for it to solve minor problems relating to emails appearing twice, not at all or it being generally confused if you updated your POP settings. The trick is to rebuild your Mailbox. This method causes Mail to delete the database and catalogue each email that you have downloaded. It will rebuild the database, so if an email appears twice or looks a bit strange this should clear it up, it also helps if you can’t find an email when you search for it.
To rebuild mail’s mailbox, select the mailbox you want to rebuild from the sidebar. Then go to Mailbox in the menu bar and select rebuild.
Mail will proceed to rebuild the database. Depending on how many emails you have this can take from a few seconds to a couple of minutes. During the process Mail will behave a bit strangely however it will return to normal when the process is finished.
When the process if finished, I recommend restarting Mail so the changes take effect. Everything should be back to normal.