Cooking does not alter the calcium in milk. Calcium from milk in baked custard stays in the same form as calcium in fluid milk. Minerals are usually pretty stable to most cooking methods.
The absorption of calcium can be decreased by oxylates in green leafy vegetables or by phytates in bran. A high protein eating plan or large intake of carbonated beverages, both high in phosphorus, increase calcium excretion because you do not have any hormones in your body to regulate phosphorus. Your kidneys regulate how much phosphorus is in your blood. When phosphorus gets too high, your kidneys excrete the extra. Unfortunately, phosphorus and calcium are closely associated and calcium gets excreted along with the phosphorus.