Second Pass: Indexes
During its second pass, Chkdsk examines each of the indexes on the volume and displays the percent of verification that is complete.
Indexes are basically NTFS directories. The percent complete is the percent of the volume's folders and the objects in those folders that Chkdsk has checked.
During this pass, Chkdsk checks for internal consistency and verifies that every file and folder that is represented by a file record segment in the MFT is referenced by at least one directory. In each one of these directories Chkdsk then confirms that every subfolder or file that is referenced actually exists as a valid file record segment in the MFT and also checks for circular directory references. Finally, Chkdsk confirms that the time stamps and file size information for the files are up to date in the directory listings for those files.
At the end of this phase, Chkdsk has achieved two objectives:
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It has made sure that there are no “orphaned” files (that is, files for which there are legitimate file record segments but for which there are no listings in any folder). An orphaned file frequently can be restored to its correct folder if that folder still exists. If the folder no longer exists, Chkdsk creates a folder in the root directory and places the file there.
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It has made sure that all directory listings are for legitimate files. If Chkdsk finds directory listings for file record segments that are no longer in use, or for file record segments that are in use but that do not correspond to the file that is listed in the directory, Chkdsk removes the directory entry for the file record segment.
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