Removing my HDD before upgrading

So following this thread https://www.reddit.com/r/Windows10/comments/3gfimj/upgrading_from_w7_with_two_harddrives/

I am about to upgrade but I want to perform a clean install on the SDD as it's getting cluttered, problem is when I disconnect my other HDD I get the "insert boot disk" error even though W7 is installed on the SDD, help!