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The low temperature heat capacity of amorphous materials reveals a low-frequency enhancement (boson peak) of the vibrational density of states, as compared with the Debye law. By measuring the low-temperature heat capacity of a Zr-based bulk metallic glass relative to a crystalline reference state, we show that the heat capacity of the glass is strongly enhanced after severe plastic deformation by high-pressure torsion, while subsequent thermal annealing at elevated temperatures leads to a significant reduction. The detailed analysis of corresponding molecular dynamics simulations of an amorphous Zr-Cu glass shows that the change in heat capacity is primarily due to enhanced low-frequency modes within the shear band region.