|You should be able to access the file/folders on the second drive but you may need to take some extra steps. |
I recommend that you disconnect the second drive before formatting the primary drive.
One important thing to check BEFORE taking any action. Verify the second drive is formatted as a basic disk.
You are positive you have TWO hard drives and not just 2 partitions on ONE hard drive. In both cases you will have TWO drive letters.