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I dove on Molasses reef a few times this year and it was quite alive, at least where I saw it. Quite a bit of coral - perhaps not the kind of stuff you see in Caribbean (no native elkhorn) but nice coral nevertheless.
It is true that some reefs around the Keys are fairly dead (American shoal is all seaweed for example, and Alligator reef is spotty). Others are in pretty good shape - Molasses seemed to be the latter as is Looe key.