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PowerShell: Recursively taking ownership of files and folders and adding permissions without removing existing permissions

This is every file server admin's nightmare: hundreds of shares, thousands of folders, hundreds of thousands of files - and custom or not inherited rights on many of them. Terabytes of data that need auditing - e.g. to find customer data, or credit card information. How do you go about accessing all the data in all the trees? What about backups failing because someone removed the System account? Of course you can seize control of the folder by taking ownership and pushing down from a top level - but how do you preserve the existing Access Control Lists?