We study symmetric vortex merger in quasi-geostrophic flows using numerical simulations with high vertical resolution. We analyse the effect of varying the vertical aspect ratio of the vortices and compare with the barotropic case. During the merging of potential vorticity cores with small aspect ratio, we observe the birth of secondary instabilities on the filaments. This is a new phenomenon not seen in baroclinic simulations having low vertical resolution. Passive Lagrangian tracers are used to explore the transport of fluid parcels during vortex merger, to provide a detailed view of the flow evolution, and to determine the value of the critical merging distance for baroclinic vortices.