The problem was that the object and collection pointers in Base and LayerCollection would get lost of file read. Normally such ID pointers would be resolved by pointing to an ID_ID placeholder which has the datablock name, and then replacing it will the real datablock. However ID_ID is only written for directly linked datablocks. This adds the concept of an indirectly linked datablock with a weak reference to it. For this we write an ID_ID_WEAK_REF code, which is a reference that will only be resolved if the datablock was read for another reason. Differential Revision: https://developer.blender.org/D4416