You may have your email set-up as IMAP on your device. This means your emails are still stored on the server even if you delete it from your Mobile device. You can set-up POP3 instead, this will keep all your emails on your Mobile device and any changes made will also change on the server.
I'd suggest checking out Setting up Optusnet Email - POP3 VS IMAP Yes Crowd post for further detail on the differences between both.
Please also keep in mind, any changes made can take up to 24 hours to reflect against your mailbox quota.
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@MjenkinsBefore re-configuring to be POP3 make sure you read the downside section very carefully.
You may want to read the following post's solution and see if you are having the same problem: