Chkdsk only reports bad sectors, it does not and cannot repair them - they are physical damage, not filesystem damage. Using chkdsk /r locates any readable information from damaged sectors and rewrites them to mapped good sectors and will repair the associated MFT entries accordingly.
Bad sectors = physical damage - can only be repaired by replacing the mechanical components of the drive. It's never done because it is not economically viable to do so. I do not use or believe in hard disk 'regeneration tools', I've never known them to work in the long term and they can mask a failing hard drive to the point where it fails totally and results in catastrophic data loss.
Filesystem damage = software damage - It can often be repaired with system level tools such as chkdsk, but it should not be regarded as a panacea and do not rely upon it to keep fixing errors caused by a failing hard drive. Filesystem damage is not always caused by hardware faults it can be caused by improper shutdown, power outages, virus infection amongst others. If filesystem damage is caused by a failing hard drive i.e. chkdsk is reporting bad sectors, the the best option is to replace the failing hard drive as it is likely to degrade further in the short term with the risk of total data loss.
If you sector clone a hard drive with filesystem damage, however caused, the filesystem damage will still need to be repaired on the cloned drive although some commercial cloning tools such as Acronis & Symantec Ghost will attempt to repair MFT errors as a pre-process to the actual clone.
