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Dear Chris Bolton1,
Thank you for reaching out to the Microsoft community. We are delighted to offer our assistance.
If you choose Keep Both, one of the folders will be renamed automatically like Folder(1). You need to move the files in Folder(1) to Folder manually and then delete Folder(1).
Thank you for your understanding and cooperation! Have a great day.
Sincerely,
Sean | Microsoft Community Moderator