may help
I understand why--its called paranoyyyaaa--and I get it too.
My friend, if you have a western digital, they suggest to do exactly that, disconnect the other HD before installing new OS\
see;
Disconnect any secondary hard drives (internal or external) from their data cables before starting the Operating System installation process. Data may be written to these hard drives during the Operating System installation process. These secondary hard drives should only be connected back into the computer once the Operating System and system drivers have been completely installed and updated.
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you are not alone