The root of the issue was caused by the dependency graph using ID pointer to map evaluated state from old depsgraph to new one upon relations update. This was failing when IDs were re-allocated rapidly: was possible that Object ID's evaluated state assigned to Mesh and vice versa. Now depsgraph uses Session UUID to identify which IDs to restore evaluated state to. The session UUID is stored in the IDNode, so that id_orig is not dereferenced on depsgraph update since the ID might be freed. The root of the issue is identified by Campbell, original patch was done by Bastien, thanks! Also thanks to Oliver and Ray and everyone else for testing!