Pre baked cake won't go dry just from being baked again, though it might be easy to overbake the new cupcake, as Joe mentioned, since the amount of batter is much less.
Cake doesn't change just from being overcooked (well, browning happens - but I mean not becoming tough or anything) - the drying out is purely mechanical, and reversible. Many baked goods can be reconstituted from being dried or stale by the addition of heat and moisture - so if your cakes were dry to begin with, the re-baking should actually help.
So, the moist batter you surround your cake in will keep it cool and moist while the batter itself bakes, and also layer on top of the cake to prevent browning from direct heat. The inner cake will only become dry if there's no moisture left in the batter - and moisture travels back and forth, once the batter is cooked, so both will be moist or dry to the same degree. As long as the cupcake isn't itself overbaked, the inner cake will be just fine.
As for chocolate, that's kinda a different question altogether and you'll get better answers if you ask it separately - but in brief, the most important thing about keeping chocolate suspended in batter is the thickness of the batter, with the weight of the chocolate coming second. A melting disk, should be thinner and lighter than a Hershey kiss (unless I'm recalling a different thing), and the wider and flatter shape should be easier to suspend in the batter - that is, if it drops through the batter to the bottom, the kiss would also have settled to the bottom.