Baking – Will chocolate eggs inside a cupcake melt when baked in the oven

It depends on what you're doing with the chocolate.

If temperature isn't that critical and its going to be mixed into a cake or brownies or such, then do it in the microwave. Its simpler and as long as you don't rush it, its does a good job. Just go 10-20 seconds at a time, in bowl that doesn't hold heat well.

If you need precise temperature controlled chocolate (for tempering perhaps), its best to use a double boiler. The bottom pan just has steaming water - so I never really count that as a dirty dish. With the double boiler, you get several advantages. It won't get any hotter than the water. It its gradual and gentle. And you can monitor and stir as the temperature rises. If it turns grainy, its likely a bit of water dripped in. Depending on the top bowl on the double boiler, its possible to accidentally knock some condensation into the chocolate...and now its toast. I use a top bowl that has a small outer lip on it to keep this from happening.

Your recipe doesn't specify 55°C, and I'd be surprised if 5–8 minutes over barely simmering water only gets that hot. Indeed, checking for sources:

• McGee, in On Food and Cooking, says:

  When the temperature reaches 120°F/50°C, high enough to unfold some of the yolk proteins, the mix thickens, traps air more efficiently, and begins to expand. As the proteins continue to unfold and then bond to each other, the foam rises into fluffy mounds. The key to maximally light zabaglione is to stop the heating just when the foam teeters on the cusp between liquid and solid. Further cooking will produce a stiffer, denser, eventually tough sponge as the proteins over-coagulate

  so that leads to the conclusion that 55°C wasn't hot enough, as it hadn't yet reached "the cusp between liquid and solid".

• Hans-Dieter Belitz, Werner Grosch, and Peter Schieberle say in Food Chemistry:

  Egg yolk can be whipped into stable foam only at higher temperatures (optimum 72°C), the volume increasing about sixfold in the process. Above the critical temperature, the volume falls and the proteins coagulate. The protein coagulation is prevented by reducing the pH value, e.g., by the addition of acetic acid. This effect is used in the production of highly stable sauces

  so that'd imply you want 72°C, or maybe higher due to the acid (wine) present. As a side benefit, that'd also pasteurize the eggs.

In summary, I think you should have cooked it hotter.

I doubt it is going to firm much in the fridge, hopefully it is stable enough to not further liquify.