No, it will be fine. The old Windows drive will just show up as another drive with your old files. In the BIOS, the Primary drive running now is set as the boot drive, so it wont even look at the second drive unless the BIOS settings are changed.
It will show up as a second HDD, that can be accessed and/or formatted. I am currently running 1 SSHD and 2 HDD's in my desktop and 1 SSHD and 1 HDD in my laptop.