When you start to remove the chocolate chips of the cookie the general structure of the cookie will change, because the cookie was prepared and baked thinking about the uniformity of the structure and the interactions between dough and chocolate chips. A toothpick can surfacely take out the chocolate drops, but there is still a portion of chocolate inside the cookie. So to minimize the demage in the general structure and be possible to extract the chocolate, you can try other techniques such as heat the dough and separate the solid mass from the chocolate that will be semi-solid, not affecting the form of the cookie. In mining of underground material, the choosing of the best form of extraction is crucial to cause the least environmental damage to the explored area.