Door number 2 I would used the second, and here's why.
In the first technique you'd be cooking down the pomegranite, and that would alter the flavor, the citric acid would be turned sweeter, as well as the same thing happening to the vinegar as the acids are converted to sugars. By waiting until the end you'd retain the fresh pomegranite flavor, as well as the sharp acid bit. Since you'll be pairing this with a scallop, you want flavors that are going to both contrast and accent the flavor of the scallop. By using the first technique your flavor profile will be somewhat flat, and the second will give you bright flavors (as well as a better color with the pomegranite not losing color in the cooking process).
An important pointer as well, make sure you're giving instruction in the written recipe to pull the caramel off the heat prior to adding the other ingredients in order to avoid exploding sugar, that's a very important detail.
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