Hi @thopulou duo ,
Did the issue occurred on all users who have messages with custom properties in your organization?
Please kindly understand here we mainly focus on general issue on Outlook desktop client, I know little about development and couldn't test with those emails that have custom properties, I have also tried to researched a lot about it but still in vain, if you still need more specific information about the message with custom mapi properties, it's suggested to add more development tag under your post.
Also, in the point of Outlook, for the requirement of clean up duplicates message, if the feature of clean up folder indeed couldn't work on your messages, we could also clean up it mannually after you change the message view and sort it, for more information, you could refer to this article.(Please Note: Since the web site is not hosted by Microsoft, the link may change without notice. Microsoft does not guarantee the accuracy of this information.)
Hope that would be helpful to you.
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