I'm going to decline writing what CHKDSK does and note it won't repair damaged files or a damages OS. For that the tools vary with the OS. Sometimes it's SFC /SCANNOW and for other OSes it's something else.
With all the malware out there, CHKDSK is only a minor tool in the kit.
Recently because of serious system instability, I ran chkdsk to see if the problem was related to bad clusters. Of course Chkdsk found a string of errors, reporting things such as "deleting corrupt attribute record...", "deleting index entry...", and so on. After a long wait, the system rebooted, but I found my system even more unstable. Later I found out through the Event Viewer that Chkdsk did 'something' to numerous files in attempt to repair them. Among those were Windows core system dll's. When I tried to look for those files, they did not exist anywhere on the hard drive.
I am afraid that maybe Chkdsk didn't do a good job repairing the flies. Perhaps what Chkdsk did was just overwriting the bad sectors? I thought at least Chkdsk could move the file segments on that specific sector to another healthy sector to maintain file integrity. I dare not to use Chkdsk again in the future, lest it should delete files by accident, rendering software, personal data, or even Windows useless.
My question is: should I expect Chkdsk to repair the hard drive while also maintaining data integrity? Or is there any other way to do exactly the tasks mentioned above?