Students typically experience a sequence of required courses. These courses are generally taught by different instructors with different pedagogical strategies and in some cases different emphases on what students should know and how they should know it. However, there are few published studies on the impact of the switching course type on learning outcomes. In this report, we use a unique research opportunity that allows us to investigate a two-semester course sequence in organic chemistry where both traditional and transformed courses were taught. We followed students over two semesters in both the transformed and traditional courses to characterize (1) students' use of mechanistic arrows to predict products and (2) how students constructed causal mechanistic explanations for simple S[subscript N]2 reactions. Here, we report how students who switched course type from the first to the second semester accomplished these tasks compared with their peers who took the same approach for both semesters. At the end of the course sequence, we find that students who switched course type performed similarly to their peers in the course type into which they switched. In particular, students' use of arrow pushing and mechanistic reasoning decreases when they switch from a transformed course where mechanistic reasoning is emphasized compared to the more traditional course. It appears that students adapt to the course culture and assessment strategies used in each course type, resulting in an apparent loss of learning gains associated with the transformed course. This suggests that systemic change cannot be accomplished in a fragmentary fashion; a more coordinated and coherent approach is necessary if improved learning outcomes are to be attained and reinforced.