Just like @ak47jar3d mentioned, you shouldn't face any issues accessing your secondary HDD drive even with the new motherboard and OS. However, you might face issues with some of the programs as the new OS and motherboard would require you to reinstall the software as well. You shouldn't have trouble with your media files, though. If you have any important data on the SSD as well, you should back it up before beginning the Windows installation as it would completely reformat and erase all data on the SSD.
Best of luck!