Hello Nick,
Do you mean you're considering swapping the two system drives around? If so, you might get away with it (after letting the two Windows installations repair/update themselves for the new drivers needed, and after reactivating the Windows licences, assuming they aren't OEM licences), but personally I wouldn't risk it (including potential risk of reliability issues resulting in the future); I would always prefer to reformat everything and re-install from clean in that situation, for good measure. Clean Windows installations perform better and more reliably anyway (regardless of moving).