Is it possible to run an unattended chkdsk?

Yes. From a command prompt run: chkdsk C: /F /R

This assumes that you want to run it on the C: drive and you want it to fix errors and relocate data from bad sectors. Since Windows will not be able to lock the C: drive it will prompt you regarding whether you want to run it at the next reboot or not, select Y for yes. This will require no user input when it runs.