We present updated magnetic field maps of the chemically peculiar B9p star $\alpha^2$ CVn created using a series of time resolved observations obtained using the high resolution spectropolarimeters ESPaDOnS and Narval. We compare these new magnetic field maps with the original magnetic Doppler imaging maps based on spectra recorded with the MuSiCoS spectropolarimeter and taken a decade earlier. These new maps are inferred from line profiles in all four Stokes parameters using the magnetic Doppler imaging code INVERS10. With the addition of new lines exhibiting Stokes $IQUV$ signatures we have a unique insight into how the derived magnetic surface structure may be affected by the atomic lines chosen for inversion. We report new magnetic maps of $\alpha^2$ CVn created using strong iron lines (directly comparable to the published MuSiCoS maps), weak iron lines and chromium lines, all of which yield a magnetic field structure roughly consistent with that obtained previously. We then derive an updated magnetic structure map for $\alpha^2$ CVn based on the complete sample of Fe and Cr lines, which we believe to produce a more representative model of the magnetic topology of $\alpha^2$ CVn. In agreement with the previous mapping, this new updated magnetic map shows a dipolar-like field which has complex sub-structure which cannot be explained by a simple low order multipolar geometry. Our new maps show that regardless of the atomic line or species choice, the reconstructed magnetic field is consistent with that published previously, suggesting that the reconstructed field is a realistic representation of the magnetic field of $\alpha^2$ CVn. $\alpha^2$ CVn is the first Ap star for which multiple, high resolution magnetic maps have been derived, providing important observational evidence for the stability of both the large and small-scale magnetic field.