Adding permissions at top level folder

Let's say your top-level folder is d:\filestore\   You add Domain Admins to it with Full Control.
If the sub-folders have maintained inheritance of the perms from that folder then you're good. 
However, if any of the subfolders have broken permissions, either by removing all permission and adding new ones or by copying the permissions and adding additional ones, then you're kinda screwed. Enforcing inheritance of the perms from your top level folder on that mess will almost certainly obliterate the existing permissions.
If you're semi-lucky you might be get away with finding a number of folders that you can apply the perms to that will then propagate to the rest.
If you're really unlucky, and it sounds like you are, then you may have to apply the permissions to many individual folders. 

I have just migrated to a new 2012 R2 server and have my AD and file server on separate VM's.  The previous server had the local Administrators group listed, but now I need to add the Domain Admins group to the top level of the folder tree and have that pass down throughout all other folders.  But I don't want it to overwrite the existing permissions.  Is there any way to do this?
The folder structure is insane and I want to redo it a better way, but that will take time and the OK from management.  There are so many "individual" users added to many folders that it is currently impossible to keep track of.  
This topic first appeared in the Spiceworks Community

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