As Allan has stated, running chkdsk every so often is a routine maintenance strategy. However, if your system has at any time suffered an untimely shutdown, such as a power blackout, a BSOD, or someone has turned off the computer using the ON/OFF button, then you should run chkdsk after any such event to repair possible file system errors.
You asked: "Can running chkdsk cause any harm to the file system?"
Yes it can, most definitely! You should exercise appropriate caution.
In the event that your hard drive has one or more bad sectors, running chkdsk /r will attempt to repair the file system error(s) and also attempt to recover data from failing areas of the disk and write that data elsewhere on the disk. This may
sometimes result in the loss of data, sometimes a catastrophic loss of data. The Windows system may be rendered unbootable. Running chkdsk with the /r switch does carry an element of risk associated with it.
Reference: DjLizard's data recovery guide
- Scroll part way down the page and read under the heading chkdsk /R.
Despite DjLizards's caution, I do occasionally use chkdsk with the /r switch, but mostly choose to use chkdsk /f ... and ONLY when I am 100% confident that there is no problem whatsoever with the hard drive