Cooking chocolate tends to have less cocoa butter than eating chocolate, which raises the cooking chocolate’s melting temperature and makes it more difficult to melt.
However, the chocolate will still melt in the oven. The chocolate chips in your cookies are simply held in shape by the surrounding cookie mixture. When the cookies cool, the chips solidify again, so it looks as if they never melted.
Dr Emma Davies is a science writer and editor with a PhD in food chemistry from the University of Leeds. She writes about all aspects of chemistry, from food and the environment to toxicology and regulatory science.