If MUA (Outlook in your case) are configured to access mailbox via IMAP protocol, it will compare local messages and the ones on server, remove local messages if they're not exist on server, and retrieve non-local messages from server, until it's fully synced.
I don't know how to tell Outlook (IMAP) or other (IMAP) MUAs not to delete local messages if they don't exist on server. Maybe you can check whether Outlook offers such feature in the preferences/settings page.