I know that rewritten entity system code has not been properly debugged yet but I'll throw it out here (sadly, cannot catch streams live due to time zone differences) in case it helps saving some time. I think there is a bug in BeginLowEntity where StorageIndex is set before entity is cleared (handmade_world_mode.cpp:18 in that day's source code).
While we're at it, I think PackSize in PackEntityIntoChuck might also be incorrect (handmade_world.cpp:222). It should probably be sizeof(*Source) since Source is a pointer.