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Dear respected Lee,
Thanks for posting in our community.
Based on the description, it seems like you have checked the Recycle Bin and Second stage Recycle Bin while neither shows the deletion logs for that folder.
Then, I want you to try the audit log search tool in Microsoft 365 Compliance centerto check the deleted file activity in your organization. (Note need admin permission to access it)
If there still shows nothing, the best way to troubleshoot the issue further is to report it to Microsoft related team, as the support team has higher permission to remotely assist you, they may collect background logs deeper. They have more resource and necessary investigation tools to help you find the root cause and fix the issue from back end. This would be the most efficient way in handling this case for you.
Microsoft 365 admin has right permission to contact related team, therefore, we sincerely recommend you use Microsoft 365 admin permission and follow steps in this **** article **** Get support - Microsoft 365 admin | Microsoft Learn **** raise a support ticket and contact Microsoft related team.
Feel free to come back with us if there have anything else I can do for you and we will offer the further support as much as we can. I appreciate your time and effort on checking these above and thank you for your time and cooperation. I hope that you are keeping safe and well!
Sincerely,
Mia | Microsoft Community Moderator