The Pythia8/Angantyr model for heavy ion collisions was recently updated with a mechanism for global colour reconnection. The colour reconnection model used is QCD colour algebra inspired and enhances baryon production due to the formation of string junctions. In this paper, we present updates to the junction formation and string fragmentation mechanisms, connected to heavy quark fragmentation. This allows for the simulation of heavy quark fragmentation, using junction formation, in heavy ion collisions. The framework is validated for proton collisions, and we show results for charm baryon production in proton-lead collisions.