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Multiple Partition Backup?

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I have two separate disks (an SSD for boot and an HDD for storage). Would it be ok for me to select the option to back both disk even though they are two separate disks and not one disk with two partitions? Or would it be better for me to backup the SSD and HDD separately?

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That's a novel question! I would back up each disk separately, which would then give you more flexibility as it's likely you'd need to restore only one at a time. For instance, if your system drive failed, you'd restore just that (likely the SSD, I assume) and not need to touch the larger HDD. I'll be interested to see if other MVPs have other thoughts.

Hmm ok... so what if I were to install programs on it like a game (because of the limited space of my SSD). I'm sure it would change the OS registry settings, so would it be necessary to restore it along with OS?

I usually recommend creating backups of drives separately just because provides more flexibility (and sometimes safety). For example, you may want to back up your Windows partition every day and your big "data/game" drive once a week. It's more personal preference, though, than right or wrong. Having both drives in the backup isn't going to limit how/what you restore. However, if the backup becomes corrupted, you've lost the backup of both drives.