Doing this would definitely void your warranty. Even if you swap out one key on a white MB with a black key, and your hard drive dies, then they can deny you coverage since you have "tampered" with the machine; even if it is completely unrelated to what you did. It could go either way, but don't expect them to cover the machine even though, "it's just one/two/however many keys you swapped out".
99% of the time keys don't just fall off, so you probably won't be able to make that claim as to the reason some keys are swapped. You might be able to say that the current MB you own replaced the previous one you had that broke, so you decided to personalize it by swapping out keys. I imagine still, that depending on what "genius" you get, they could still deny coverage.
If you swapped out the entire topcase then there would be no debate as you have obviously opened up the machine. If it was done by an authorized repair center, Apple could still deny coverage, though you could claim ignorance, or if you had proof that the provider told you it would still be covered under warranty.
At my job at an authorized Apple repair shop, we would advise customers who, still under warranty, wanted to install a larger drive in their laptops to keep the old drive just in case. If they needed to send their machine off to Apple, we would install the old drive back in so they wouldn't be denied coverage based on non-original hardware.
*This is all considering you go to Apple. If you go back to the authorized provider that replaced your topcase, they can still perform warranty service for you. As long as they don't need to ship the laptop off to Apple (which happens), they can perform all the repairs in house, and Apple will never see it. What they don't know, won't hurt them, and personally I don't think it's a big deal. If we ever did upgrades or customizations like this at our store, we told people that that, "it just depends whether or not Apple will consider the warranty voided for this. If you have a problem, just come back to us".