Having NTFS permissions that are messed up is a HUGE headache. Fixing them means trying to trick NTFS into letting you do what you need to, and sometimes it just won’t let you. Below is my nuclear option that will, at least, get you back where you can make the necessary changes to get what you need set.
Download the NTFSSecurity powershell module, unblock the zip file, then extract it to C:\Windows\System32\WindowsPowerShell\v1.0\Modules
Make sure that the top level folder has the permissions you want to inherit. Make sure you have permissions on this top level folder.
Run Powershell as admin.
Run the following commands in the folder you want to propagate inheritance down from:
get-childitem -recurse | Enable-NTFSAccessInheritance
You may have noticed that since Server 2012 R2, signing in with a local admin account (that isn’t .\Administrator) doesn’t run Windows Explorer as an admin. You’ll be logged in, of course, but File Explorer won’t be running with elevated privileges, and that means that you can’t change security ACLs on files through the GUI.
As it turns out, it’s pretty easy to fix this on a session-by-session basis.
Fire up Powershell as admin (for some reason this doesn’t work in CMD and I haven’t had the brain space to figure out why) and run the following:
taskkill /f /FI "USERNAME eq $env:UserName"/im explorer.exe
That will kill the exiting explorer session for you (and it won’t restart, as it’s wont to do if you kill the process through task manager).
Then, run the following:
That’ll fire up explorer again, but this time you’ll be able to open File Explorer with your admin privileges and make changes as necessary.