A group of Microsoft Products and technologies used for sharing and managing content, knowledge, and applications.
Dear Bassey,
Good day!!
Apologies for the inconvenience caused and please don’t worry, let’s work together on your concern and move towards a resolution path.
I understand your concern and to my knowledge, the duplicate folders or files in the SharePoint Online Document Library or OneDrive for Business will be caused due to the sync issues in the users OneDrive sync client and I am sorry to convey there is not direct tool in the Microsoft 365 to delete the duplicate folders or files, where we need to manually delete the duplicate folders or files.
Moreover, I would like to confirm whether the duplicate folders or files in the SharePoint Online is created by the system account or any user account. If it’s any user account, then please try to reset the OneDrive sync client and see whether the same problem happens: Reset OneDrive - Microsoft Support
Our sincere apologies if there is any misunderstanding from our end, and request you to share the more details with some screenshots which will help us to better understand and guide you further.
Appreciate your patience and understanding. Have great day!!
Best Regards,
Sophia