The electromagnetic field itself contains energy distinct from the energy of charged bodies, the energy in a given volume of empty space can be found by integrating the energy densities $\frac{1}{2}\epsilon E^2$ and $\frac{1}{2} \frac{B^2}{\mu}$ over the region. When the EM fields increase the kinetic energy of charged particles, there is a corresponding decrease in the energy of the EM field in that region, so total energy is unchanged.
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