Hi @Shanuka Thushara ,
It seems this is not a common issue per my test. However, we can work together to narrow down and resolve the situation. So, Please kindly provide more information below to let us work further.
1.What version of SharePoint are you using (sp server or sp online)?
2.Does "files are being duplicated" mean that the same file exists twice? Do they have exactly the same name and content? Are they created by the same person and at the same time?
3.Try to stop the synchronization and then run the installer again for the problematic SharePoint site. To do this, open OneDrive, click the cloud icon in the taskbar, select Settings, then Accounts, then Select Folders. Uncheck the box next to SharePoint Sites and click OK. Then, go to the SharePoint site in your web browser and click Sync to set up synchronization again.
4.Unlink OneDrive and run the OneDrive installer again. This will reset all of your sync settings and preferences, so you'll need to reselect the folders you want to sync. To do this, open OneDrive, click the cloud icon in the taskbar, select Settings, then Accounts, then Unlink this PC. Then, sign in to OneDrive again and follow the instructions to set up synchronization.
5.Temporarily move files out of the Sync folder and then move them back into the Sync folder. This will force OneDrive to resynchronize the files and resolve any conflicts or duplicates. To do this, open File Explorer, go to the Sync folder on your SharePoint site, select the files you want to move, and then drag them to another location on your device. Wait for OneDrive to finish synchronizing, and then move the files back to the synchronization folder.
6.Make sure SharePoint Online and OneDrive support file names and file types. Certain characters, symbols, or file extensions can cause synchronization errors or duplication issues. You can find a list of unsupported file names and file types here.
Hope the information can help you. And if there have any unclear or misunderstanding, please feel free to post back and we’ll continue to help you all the time!
Your understanding and patience will be highly appreciated! Hope you have a good day and keep safe!
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