That is far too long. Even with USB 2.0 at 33MB per second it shouldn't take more than 19 hours. It is ok to stop it since chkdsk is primarily just reading. It is when it encounters a bad sector and preps your file system to mark it as bad is when you don't want to close it.
If you can stop it while it is reading you are ok. Closing the command line doesn't always close it. You can guarantee it's closed by bringing up Task Manager. Look for 'chkdsk' and end it's process. Also ensure that no disk utilities are running then bury into your 'Services' and check that 'virtual disk' is not started.
Once you have this clean slate, I would check the drive manufacturer to see if they have any HDD diagnosis. If it's an external drive, it will run much faster and diagnosis will be more reliable if you can figure out how to plug it in natively via SATA. Have fun.