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The Ly α emission line is the brightest UV emission line in M and K dwarf spectra and serves as an important tool for studies of stellar chromospheres, the interstellar medium, and exoplanet atmospheres. However, Ly α observations have proven difficult due to the strong absorption by the interstellar medium, necessitating a reconstruction of the intrinsic stellar line from the observed spectrum. We have performed new Ly α reconstructions on the MUSCLES Treasury Survey stars, incorporating improved parameterizations for the intrinsic line wings and line core. We present an analysis of how the updated Ly α fluxes could impact photochemical and atmospheric escape studies and flux–flux scaling relations with other chromospheric emission lines such as Ca ii H and K. We find the overall intrinsic Ly α flux of our star sample decreases by as little as 10% to as much as ∼5× fainter compared to previous findings. The exception to this flux decrease is the M dwarf GJ 581, whose Ly α flux increased by 4%. These results will likely have a limited impact on the aforementioned studies that rely on Ly α fluxes.