We present an analysis of students' thinking skills as evidenced by free-response exam problems during the COVID-19 pandemic. We compare two inquiry-based, laboratory-based classical mechanics courses, one taught online and one taught in person during the pandemic, and two inquiry-based, laboratory-based electricity and magnetism courses, one taught online and the other in person during the pandemic. We use a rubric that was previously developed based on Bloom's taxonomy (revised version) to compare the thinking skills of students in classes taught by different pedagogies. We discuss the method and analysis, and present results and interpretations. No significant differences were found in thinking skills between students in the online and in-person pandemic classical mechanics courses. However, we did see a difference in the thinking skills between the online and in-person pandemic electricity and magnetism courses as the semester progressed.