3 Answers. Under normal circumstances, it's perfectly safe as long as you're using the one designed for your version of Windows. However, it is possible that there are important files on the bad clusters, which haven't been marked as bad, and those clusters may be working intermittently.

Can chkdsk be harmful?

CHKDSK is able to check your drives for errors. Yet, if misused, it will cause unrecoverable damage to your drives. ... Windows has a native disk repair tool – CHKDSK, which is really robust to detect bad sectors and fix disk errors. However, it may result in some troubles and risks when it is misused in some cases.

Should I use chkdsk R?

You should use chkdsk occasionally on FAT and NTFS file systems to check for disk errors. Chkdsk examines disk space and disk use and provides a status report specific to each file system. The status report shows errors found in the file system. ... Chkdsk corrects logical disk errors only if you specify the /f parameter.