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Dear Ralph ,
You can create the flow as follows.
Trigger: When an item is created.
Condition: If the folder isn't created by the library owner
If the item is a folder
If the folder path is libraryname/
Action: If yes, delete the item. If no, leave the item.
The flow will automatically remove the top folder which is created by users and will leave the files which is created by the users and leave the subfolder which is created by the users.
Sincerely,
Cliff | Microsoft Community Moderator