CloudExtend differentiates between files and folders that are attached vs those that are associated with NetSuite records. If you have attached a file and subsequently attach the file's folder to the same NetSuite record the file will appear at both the root level (because you directly attached it) and under the folder (because it's associated with the folder).

You use CloudExtend to Attach a file or folder to a NetSuite record, When attached, CloudExtend will show these files and folders at the root level of the CloudExtend files tab. 

Attached items are also shown with a pin icon, signifying that the files and folders are effectively pinned to the NetSuite record. Even if you move these files to a different location in OneDrive or SharePoint at a later time, they remain attached to the record.

Sub folders and files under attached folders, are said to be only Associated with the NetSuite record. These files and sub folders are only associated with the record as long as they remain under the attached folder. If you move a file/folder out of the attached folder in OneDrive or SharePoint you will find that  the item is no longer associated with record in CloudExtend. This characteristic is indicated by the lack of a pin icon on the item.

If you have attached items inside of an attached folder then they will also be treated as pinned and such items would appear both at the root as well as under the folder.