We present an update on our calculation of the short-distance $D^0$-meson mixing hadronic matrix elements. The analysis is performed on the MILC collaborations $N_f=2+1$ asqtad configurations. We use asqtad light valence quarks and the Sheikoleslami-Wohlert action with the Fermilab interpretation for the valence charm quark. SU(3), partially quenched, rooted, staggered heavy-meson chiral perturbation theory is used to extrapolate to the chiral-continuum limit. Systematic errors arising from the chiral-continuum extrapolation, heavy-quark discretization, and quark-mass uncertainties are folded into the statistical errors from the chiral-continuum fits with methods of Bayesian inference. A preliminary error budget for all five operators is presented.