In this work we demonstrate germanium loss from uncapped substrates during low temperature drive-in annealing in inert ambient. An Arrhenius law with an activation energy of 2.03 eV describes the measured loss rate of germanium as a function of temperature. Accurate simulations of implanted phosphorous profiles in nonpassivated substrates have been performed considering the extracted germanium loss rate. A capping layer on the germanium surface reduces phosphorous dose loss, with Si3N4 being more efficient than SiO2. The capping layer material also affects the extent of dopant concentration-dependent diffusion for high dose phosphorous implantation.