This paper aims to share the challenges encountered by the authors while exploring the significance of controllability in the early stage of heat exchanger network (HEN) design, particularly through the use of P-HENS – a graph theoretic-based HEN synthesis tool for multi-solution HEN synthesis. Presently, no existing studies have leveraged P-HENS-derived networks to reveal insight on how network topology affects its dynamic performance. This work began with a 5-stream problem as a base case, where P-HENS was used to generate four feasible HENs that meets the minimum energy requirement (MER). A preliminary screening narrowed these options to two configurations, which were then simulated in Aspen Plus. Bypass are added to the two selected HENs for further control studies in Aspen Plus Dynamics. The results indicated that both HENs could handle only some disturbances and return the outlet temperature to its nominal value, with some cases showing marginal deviations. Then, different bypass values (e.g., 0.1 and 0.5) were explored to analyze its impact on control performance but it reveals that even with a larger bypass value of 0.5, the HEN struggled to adequately adjust during disturbances. The findings from this work showed that the controllability of the HEN is collectively influenced by the bypass value, the temperature difference of the “direct inlet and outlet of the heat exchanger”, and the temperature difference of the “inlet streams of both hot and cold streams placed in the heat exchanger”. A generic workflow that would help future researchers avoid similar pitfalls has been presented.