But you can't boot from an external USB HDD, but you can from a USB jump drive. That's what's confusing me.
Unless the HDD you're using is a SATA (or whatever type your computer has) placed in an external case that you connect via USB, you're not going to be able to boot from it, and even then, it would have to be transplanted in to the machine in question.
I'm sure someone will correct me if I'm incorrect, but unless my memory is failing you simply cannot use an external USB HDD as a boot device.
I believe, but cannot guarantee that my memory is correct on this, that you can clone between an SSD and an HDD, both of which are installable in your machine, and have either one work regardless of what the "usual drive" happens to be. I can't imagine that everyone who's invested in an internal SSD to replace their HDD gets a second SSD to do clones. You could use the HDD that you just removed, when the next clone time comes, connected to the machine via a USB cable or enclosure to clone to and it should function if plugged in were the SSD to fail.
Brian AKA Bri the Tech Guy (website in my user profile) - Windows 10 Home, 64-Bit, Version 1803, Build 17134
. . . the presumption of innocence, while essential in the legal realm, does not mean the elimination of common sense outside it. The willing suspension of disbelief has its limits, or should.
~ Ruth Marcus, November 10, 2017, in Washington Post article, Bannon is right: It’s no coincidence The Post broke the Moore story