If theres no operating system on the larger drive it should work cloning one to the other, but its not strictly necessary, if you can connect the second drive there nothing stopping you booting into windows using the smaller drive and then using the second drive to save any files to, way my computer is set up at the moment i have a 80gb drive with the os and several tb drives with everything backed up on them, reason i do it is if anything goes wrong with my os or i want to install a different os everything is still saved on a separate drive and im not having to copy hundreds of gb of files to c drive every time i reinstall
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