When using the same POP3 email account on more than one device, email messages may appear only on the first device that receives them. This occurs when an email client is configured to automatically remove email from the server after an email client has received it. You can configure your iPhone, iPad, iPod touch, or Mac either to keep a copy of the email on the server, remove it after a certain number of days have passed, or keep it until you move it from your inbox.
By default, Mail will only delete messages from the server one week after deleting the message from the device. This setting is appropriate for most users, but can be changed when necessary.
1) In Settings, select Mail, Contacts, Calendars.
2) Select the account for which you wish to change the settings.
3) Select Advanced, located at the bottom of the list.
4) Select Remove.
5) Select a time frame :
Never: The email message will remain in place on all of your devices and email clients.
After one day: One day after Mail reads the email message, Mail will remove the message from the server. The message will exist only in Mail, not on any other clients.
After one week: This setting works the same as "After one day", except that Mail waits one week.
After one month: This setting works the same as "After one day", except that Mail waits one month.
6) Select Advanced and tap Done to save your settings.