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Thank you for sharing your findings.
Based on the information you've provided, it does appear that the affected messages are being presented in the mail-enabled Public Folder with the MSGFLAG_UNSENT (0x8) already set, likely as part of the delivery or processing pipeline
The more important question is why some messages end up with that flag while others do not.
Since you've already confirmed that attempts to clear the flag are unsuccessful, there does not appear to be a supported administrator-side method to correct this for existing items.
Instead, I would suggest focusing on identifying differences in the message processing path. In particular, look for any common factors among the affected messages, such as:
- Mail flow rules (especially disclaimers / banners that rewrite the message body)
- Other transport rule actions that modify messages (e.g., subject prepend, header changes)
- Defender for Office 365 processing (Safe Attachments)
As a test, if possible, try excluding the affected Public Folder from disclaimer or banner rules and compare newly delivered messages with those that follow different mail flow paths.
If the issue only occurs when messages are modified during transport, this would indicate that the behavior is tied to the delivery and processing pipeline rather than the Public Folder itself.
Unfortunately, if Exchange Online continues to store or reapply the UNSENT flag during delivery, there may not be an administrator-controlled way to repair existing items. In that case, the next step would be to open a support case with Microsoft so they can trace the message processing path and confirm what is setting the flag.
As we're not Microsoft Support, this is a user-to-user forum, we cannot verify whether this is a confirmed service issue. However, your findings strongly suggest that the flag is being introduced during message processing in Exchange Online rather than by any post-delivery action.
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