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I may not be understanding you correctly but I think you're asking if you can have a completely seperate install of your operating system with all your astro software on an external usb drive so you could boot straight into that and basically ignore whatever is on your internal drive...?
If so this should be possible. I'll assume you're talking about running Windows and it is possible to install on a usb drive. (this would also work with linux, I don't know about OSX)
Your bios will have to be able to boot from usb but unless it was made last millennium it should.
Also you would want it to be on a pretty fast drive and preferably through usb3 otherwise it's going to run pretty slowly.
I once had a linux install on an ExtremeIII SD card and it ran pretty well.
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