There are hundreds, maybe thousands of backup/restore programs out there, but if the one you're using is reliable, yes that should work as long as something like a power surge or fire doesn't destroy both HDs at the same time.
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Good luck.
So a couple weeks ago I bought a second internal 1TB HD for my computer. I've been using Macrium Reflect to clone my regular drive onto my new one as a backup. However, I'm wondering is this the best way to 'back up' my main drive to the second drive? If windows has a problem/my computer won't boot, can I simply unplug the main drive and have it boot from the clone? Will it do it automatically? Or should I be doing images to my 2nd internal drive?

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