Hubble Space Telescope images of Jupiter’s UV aurora show that the main emission occasionally contracts or expands, shifting toward or away from the magnetic pole by several degrees in response to changes in the solar wind dynamic pressure and Io’s volcanic activity. When the auroral footprints of the Galilean satellites move with the main emission this indicates a change in the stretched field line configuration that shifts the ionospheric mapping of a given radial distance at the equator. However, in some cases, the main emission shifts independently from the satellite footprints, indicating that the variability stems from some other part of the corotation enforcement current system that produces Jupiter’s main auroral emissions. Here we analyze HST images from the Galileo era (1996-2003) and compare latitudinal shifts of the Ganymede footprint and the main auroral emission. We focus on images with overlapping Galileo measurements because concurrent measurements are available of the current sheet strength, which indicates the amount of field line stretching and can influence both the main emission and satellite footprints. We show that the Ganymede footprint and main auroral emission typically, but do not always, move together. Additionally, we find that the auroral shifts are only weakly linked to changes in the current sheet strength measured by Galileo. We discuss implications of the observed auroral shifts in terms of the magnetospheric mapping. Finally, we establish how the statistical reference main emission contours vary with CML and show that the dependence results from magnetospheric local time asymmetries.