Usually system restore disks delete all the information on the primary hard drive and reinstall the operating system and programs that came with your computer back to its initial state. If this were the case, your secondary hard drive would remain untouched.
There are other ways your information could be lost if stored on a secondary hard drive - accidental deletion or formatting, total hard drive failure, etc. Nothing is for certain - which is why any information important to you should be backed up and kept secure and physically separate from your original copy of the data.
