Here are some things you can do to resolve this issue:

1. Check the Deleted Items Retention period and ensure that it has not been set to 0 days.
2. Check if the user has any third party Add-ins or Antivirus software configured to scan mailbox stores.
3. Disable any IMAP or POP access to their mailbox.
4. Run the Mailbox Cleanup Tool to empty deleted items and other folders.
5. Perform an Online Repair of Office 365.