Medical decision protocols constitute theories for healthcare decision making that are applicable for "standard" medical cases but have to be adapted for the other cases. his holds in particular for the breast cancer treatment protocol, that is one of the protocols studied in the \kasimir research project. Protocol adaptations can be seen as knowledge-intensive case-based decision support processes. Some examples of adaptations that have been performed by oncologists are presented in this paper. Several issues are then identified that need to be addressed while trying to model such processes, namely: the complexity of adaptations, the lack of relevant information about the patient, the necessity to take into account the applicability and the consequences of a decision, the closeness to decision thresholds, and the necessity to consider some patients according to different viewpoints. As handling these issues requires some additional knowledge, which has to be acquired, different methods are presented that perform adaptation knowledge acquisition either from experts, or in a semi-automatic manner. A discussion and a conclusion end the paper.