Hi Matt Carter,
Welcome to Microsoft Q&A forum.
I understand how concerning this is, especially if emails are being hidden from the message list and you may miss important messages.
To narrow this down, could you please share these three quick details:
- Does the issue happen only on Outlook.com on the web (outlook.live.com), or does it also happen in Outlook mobile / Outlook desktop (New/Classic)?
- When the emails “disappear,” do you see them in Focused/Other, Archive, Deleted Items, or under Deleted Items > Recover items deleted from this folder?
Once I have this information, I can advise on the next steps.
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