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The photophysical properties of conjugated materials can be strongly affected by the nature of intermolecular interactions. Toward this aim, supramolecular self-assembly facilitates efficient packing of molecules into ordered architectures, which allows efficient intermolecular coupling. However, the resulting electronic overlap imparts additional sensitivity to the disorder, predominantly because of the "nonlocal" origins of the photophysical properties. Understanding the nature and origin of the disorder in conjugated systems is a prerequisite to exploit the benefits of efficient intermolecular coupling. In this report, we utilize chirality as a marker to sensitively probe the nature of the disorder in thermodynamically assembled helical nanoaggregates of a chiral conjugated polymer poly[(9,9-di-n-octylfluoreny1-2,7-diy1)-alt-(benzothiadiazole)] (PFBT). Surprisingly, we find that one-handed intermolecular coupling in helical PFBT aggregates leads to differences in the decay pathways of left- and right-handed excitations. We attribute the emergence of this sensitivity to the disorder in the excitonic coupling of flexible, nonplanar polymer chain conformations, likely predominant at the edges of the aggregate. Our findings shed insights into the effect of disorder on the photophysical properties, which open up new opportunities for sensitively exploring the links between intermolecular coupling and photophysical properties of conjugated systems.