Ahhh, I get it now. I was writing a post agreeing with kannibul when the answer dawned on me. See if this example helps (or tell me if I'm all screwed up).
Lets make a theoretical cylinder that has 0.6L capacity on its down stroke and 0.1L capacity on its up stroke. I'll call that a 6:1 ratio (I don't know if that is how they measure a real cylinder but it will work for this example). So when the cylinder travels down it sucks in 0.5L of air since 0.1L was already there at the top of the stroke. Now we change out the cylinder head with a taller cylinder and leave everything else the same. You now have 0.05L on the up stroke and 0.55L on the down stroke. This gives you a new compression ratio of 11:1.
Your stroke is still the same. It sucks in 0.5L of air just like the original cylinder but it squeezes it into a smaller volume.
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