This guide will let you know what is the difference between the IMAP and POP3 protocols that are related to the incoming Helpdesk mail settings.
POP3
If you set the POP3 protocol, then they will be deleted automatically from the original mailbox.
IMAP
However, if you choose the IMAP, then the difference with pop3 is that when the emails are received, they are not deleted but left in the original mailbox. Please keep in mind that they will be marked as read after being fetched to the Helpdesk.