By default, the "Flux-###.fits" and "Err-###.fits" makee output spectra wavelength scales have been corrected to the heliocentric frame of reference. Thus the motions of the earth around the sun, the earth about it's axis, and the earth around the Sun-Moon center of mass, are taken out of the HIRES spectra wavelength scale. (Note that the Sky-###.fits are NOT corrected to heliocentric.)
Since the motion of the earth about the sun is roughly 30 km/s, this correction can vary by as much as 30 pixels between two exposures taken six months apart (assuming 2.1 km/s/pixel.)