Once an email has been popped, I don't know of a way to avoid it being deleted from the Inbox if you disconnect it. It would be better to log out all agents. probably stop the ACDServer subsystem in IC System Manager, and move all the emails from the Inbox to another folder. Then restart ACDServer. If any emails continue to come to agents, let them timeout rather than connect.
That will halt all ACD processing for the server while you have ACDServer shut down, so it needs to be done during off hours.
If you can't do that, then you can have the agents forward popped emails to another mailbox, in which case they will be deleted from the original mailbox but not deleted from the system. Once the queued emails are all out of the queue, you can move those ones back to the Inbox, realizing that the From address will now be the system email, not the original sender.
Sorry I don't have a great solution for you...that's the best I can come up with for now.