Will installing Windows 7 on a system with 2 HDD's make data inaccessible?

I currently have a system running two hard drives, one with the OS (7) and one for data storage, I have loads of experience installing win 7 onto a system with a single HDD but if I want to reinstall can I backup everything (pictures, video, various other things) onto the data storage HDD and then simply reinstall onto the main drive and copy everything back over? The reason I ask is that I have heard multiple stories of data becoming inaccessible after the install. Thanks in advance.