A great variety of single- and multi-component nanocrystals (NCs) can now be synthesized and integrated into nanocrystal superlattices. However, the thermal and temporal stability of these superstructures and their components can be a limiting factor for their application as functional devices. On the other hand, temperature induced reconstructions can also reveal opportunities to manipulate properties and access new types of nanostructures. In situ atomically resolved monitoring of nanomaterials provides insight into the temperature induced evolution of the individual NC constituents within these superstructures at the atomic level. Here, we investigate the effect of temperature annealing on 2D square and hexagonal arrays of FexO/CoFe2O4 core/shell NCs by in situ heating in a transmission electron microscope (TEM). Both cubic and spherical NCs undergo a core-shell reconfiguration at a temperature of approximately 300 ° C, whereby the FexO core material segregates at the exterior of the CoFe2O4 shell, forming asymmetric dumbbells ('snowman-type' particles) with a small FexO domain attached to a larger CoFe2O4 domain. Upon continued annealing, the segregated FexO domains form bridges between the CoFe2O4 domains, followed by coalescence of all domains, resulting in loss of ordering in the 2D arrays.