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"When I re-enable it then turn mail off and back on again they reappear."
Can you please expand on exactly what you are doing here ie what are you doing here "....then turn mail off and back on again..."?
The POP email needs to be disabled sufficiently such that it is no longer able to read new email messages. If it is able to read new messages it will delete them from the Optus server. Perhaps you can put an incorrect password into the POP email's credentials which means it will be unable to fetch new messages.
Test this scenario by sending yourself an email and seeing if it arrives in the POP email. It should, of course, arrive in the IMAP email but not in the POP email.
If you are on a Mac using Mail you could try dragging a single email from the POP email to the IMAP email and see what happens.
Something that might be 'cleaner' and in addition to what you have already done is to go into Mail-> Preferences->Accounts, select the POP account and then in Advanced deselect 'Include when automatically checking for new messages'.
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