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Yes, it can be done, but it's a bit painful. There are numerous ways to make mistakes and burn a day recovering. I've never written it up so I'm hesitant to send you into a culdesac.
Is one drive all C and the other all D?
The easiest way would be like Redjake said. If you have a third drive. Even if temporarily. Clone C to X, D to C, and X to D. Exchange C and D drives (cable & master/slave positions) as needed. Done.
If you want to get sick and there's free space on one drive for the contents of the other, you could say save D to an image file on C, clone C to D, exchange hardware positions, then restore the image of D.
Clone utils can be expensive or free, though the free ones usually require a bit more care. Free ones don't generally handle image files gracefully.
This kind of thing isn't needed much anymore with the price of drives.
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There are a vast number of people who are uninformed and heavily propagandized, but fundamentally decent. The propaganda that inundates them is effective when unchallenged, but much of it goes only skin deep. If they can be brought to raise questions and apply their decent instincts and basic intelligence, many people quickly escape the confines of the doctrinal system and are willing to do something to help others who are really suffering and oppressed." -Manufacturing Consent: Noam Chomsky and the Media, p. 195
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