Pebble-scale models of the interactions inside packed beds are critical for determining alterations to thermophysical properties in the wake of changes to the packed bed due to cracking, sintering, or creep-deformation of the ceramic pebbles. Simultaneously, the helium purge gas flow through the pebble bed can change; while not specifically playing a role as coolant, it does have an impact on the thermal transport in the volumetrically heated bed. We present numerical tools that are capable of resolving pebble-scale interactions coupled to bed-scale thermofluid flow. The new computational techniques are used to show that maximum temperatures in pebble beds do not increase drastically in spite of the significant amount of cracking induced in our numerical model. Furthermore a complete flow field of helium moving through densely packed spheres is modeled with the lattice-Boltzmann method to reveal the strong effect of slow-moving helium gas on flattening temperature profiles in pebble beds with nuclear heating.