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Transmission via these interconnects can be performed more efficiently using quantum multiplexing, where information is encoded in high-dimensional photonic degrees of freedom. We explore the effects of multiplexing on logical error rates in surface codes and hypergraph product codes. We show that, although multiplexing makes loss errors more damaging, assigning qubits to photons in an intelligent manner can minimize these effects, and the ability to encode higher-distance codes in a smaller number of photons can result in overall lower logical error rates. 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