The COVID-19 pandemic created unprecedented disruptions in models for engineering student training. At The Citadel, an undergraduate-focused college in the Southeastern United States, a variety of modalities were implemented following the onset of the pandemic, including emergency online and Hyflex learning. We conducted a longitudinal study to analyze the cognitive load among our undergraduate engineering students throughout changing modalities. Using data from the NASA Task Load Index (TLX) and open-ended reflections on student challenges, we found that total workload (a surrogate for cognitive load) was generally highest during emergency online learning in the second half of Spring 2020 semester, with experiences possibly varying across different demographic and academic groups. Emergency online challenges were often related to time management, personal organization, and responsibility for learning. In contrast, HyFlex challenges were often related to technology and communication challenges. While emergency online learning was a cognitive load disruption, that disruption was often associated with personal and/or academic development. HyFlex learning mediated cognitive load disruption; although, student challenges may have been simple nuisances rather than mediators of developmental change.