Earlier the folder was ok, while applying some permission rule in sub folders this problem arose.
Sounds like you somehow managed to corrupt the file system. I would have expected chkdsk to fix that.
I can think of 2 things you can try. First try using psexec and run cmd.exe.
https://learn.microsoft.com/en-us/sysinternals/downloads/psexec
psexec -s cmd.exe
That will launch a command prompt that will be running as the system account. (Run whoami.exe). Then try the 4 commands that I posted earlier. If you still get "access denied", then I don't know what to tell you if SYSTEM can't access the files.
Chkdsk does have this switch.
/sdcleanup NTFS only: Garbage collect unneeded security descriptor
data (implies /F).
You could try that, but if the permissions are corrupt, I would have no way of knowing what that might do to your file system. Do you have a backup of the files/folders?