Disasters perturb the agri-food systems and can constrain the study of that system by limiting the researcher’s mobility. The study of complex and dynamic systems has often employed Fuzzy Logic Cognitive Mapping (FCM), and this has become a promising method of semi-quantitative modeling and collective decision-making in diverse contexts. We wanted to employ FCM to study a region in the Indian Sundarbans hit by COVID-19 lockdown and a severe cyclonic storm to identify corrective interventions. Data elicitation for FCM is commonly performed in face-to-face or workshop environments, which was not possible during the COVID-19 lockdown. We developed and applied a modified FCM method by using qualitative research and standard cognitive mapping techniques. Our study shows that shared cognitive maps can be developed from a distance involving a small number of stakeholders. Our modified methodology can be used to develop shared cognitive maps involving people separated by distance, especially during disasters.