During its third pass, Chkdsk verifies security descriptors. Chkdsk examines each security descriptor that is stored in the $Secure metadata file for each file's associations with files or folders that are on the volume.
Security descriptors contain information about ownership of a file or folder, NTFS permissions for the file or folder, and auditing for the file or folder. The percent complete is the percent of the volume's files and folders that Chkdsk has checked. Chkdsk verifies that each security descriptor structure is well formed and is internally consistent. If they are not, Chkdsk sets the permissions on the files or folders back to the default settings. Chkdsk does not verify the actual existence of the users or groups that are listed or the appropriateness of the permissions that are granted.
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