There is a pressing need in clinical practice to mitigate (identify and address) adverse interactions that occur when a comorbid patient is managed according to multiple concurrently applied disease-specific clinical practice guidelines (CPGs). We describe an automatic algorithm for mitigating undesirable interactions for pairs of CPGs. The algorithm constructs logical models of processed CPGs and employs constraint logic programming to solve them. It handles two important issues frequently occurring in CPGs - iterative actions forming a cycle and numerical measurements. Dealing with these two issues in practice relies on a physician's knowledge and the manual analysis of CPGs. Yet for guidelines to be considered stand-alone and an easy to use clinical decision support tool this process needs to be automated. In this paper we present our algorithm that aims to build such a tool by mitigating multiple CPGs while handling cycles and numerical measurements. The application of the mitigation algorithm is illustrated with a clinical case study involving a comorbid patient suffering from atrial fibrillation in the setting of Wolff-Parkinsons-White syndrome.