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Lotus Tech put it the below entry in the notes.ini
pop3markread=1
By default, messages in a mail file on a Domino 8.5x, 8.0x, and 7.0x server are not marked as READ when they are accessed by a POP3 client and left on the server. However, the POP3MarkRead parameter can cause popped messages to be marked as READ, depending upon the value of the parameter.
The POP3MarkRead parameter can use one of four values: 0, 1, 2, or 3. This parameter can be set at the Domino console by using the set config command and restarting the POP3 task, such as:
set config pop3markread=1
restart task pop3
POP3MarkRead=1 marks a message as READ when a POP3 client accesses a message on the Domino POP3 server, such as by using the LIST or RETR commands.
This stop the duplicate messages.
Feedback response number WEBB8MJQ6L created by ~Fred Umtumipulettu on 10/11/2011
pop3markread=1
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. . . . . . . . pop3markread=1 (~Fred Umtumipul... 11.Oct.11) 
