Yes, for whatever reason, the babies seem to develop only in the calcified part. However, I did see photos from a clutch recently that was almost entirely decalcified, but were normal-sized eggs. The hatchlings were typical size, they actually made it.
The thing to watch is that the decalcified part of the egg can become infected, and if the infection gets into the live part, it can kill the embryo. Try to keep it very clean, and if it starts vigorously molding, a bit of antifungal powder might be in order. It can get pretty bad, and the baby will still be fine, though.
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