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POP3 Email duplication after running mailbox store scan manually

We  are using pure message 4.0 for exchange 2013 and recently when we scanned the mailstore database all POP3 Accounts downloaded old copy of email. To verify i ran the manual mailbox store scan and again all the messages were downloaded to POP3 Account only. Is there anyway to stop this on POP3 Account as i have so duplication bacause of this



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