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Windows doesn't support being booted from a disk attached via USB, at least not out of the box. How did you get a fresh install booting from USB?
But yes, if you performed a fresh install that resulted in a dual boot setup, your second Windows install disk won't necessarily have everything necessary to be booted separately. As you see, you have a single Windows Boot Manager interface that lists both OS choices. That's because there's only one instance of Windows Boot Manager on your system, which will turn around and load whichever Windows partition you select. The reason this is done is to make it easier to manage dual boot systems, since this way you have a single instance with multiple choices rather than having to deal with having your actual motherboard boot from a completely different device if you want to switch environments (which would especially be a chore on motherboards that don't offer a one-time boot menu). But the drawback to this design is that your secondary environment isn't set up to be independently bootable.
If you want to achieve that AND run a dual boot setup for a while, I would try performing a fresh install while you don't have any other Windows disk connected so that you get a self-contained environment on that secondary disk, then reconnect your main Windows disk, at which point you may be able to use a tool like EasyBCD to add your secondary Windows environment as an option in your primary Windows disk's Windows Boot Manager instance. In that case you'll be able to boot the secondary disk either way.
But based on your final questions, I'm not sure what you're trying to achieve here. Are you trying to run a long-term dual boot setup, or are you trying to set up a new Windows environment to replace your existing one? Those are two very different goals. It sounds like you want a dual boot setup, but then I'm wondering why you're asking about overwriting your current drive with this new one.