Abstract The cold-classical Kuiper Belt Object 486958 Arrokoth is a contact binary composed of two flattened lobes, Weeyo and Wenu, closely aligned along their principal axes, despite each lobe having a highly irregular shape. The object’s smooth and relatively undamaged structure suggests the observed bilobate shape results from a gentle, low-velocity merger between the lobes. The existing hypotheses to explain such a merger include orbital energy dissipation from the protosolar nebula gas drag and Lidov–Kozai (LK) oscillations originating from an initially ultrawide binary. However, what is missing is how mutual dynamics due to the lobes’ shape irregularities impact their final orientations at the time of the soft merger. Here, we show that none of the proposed orbital evolution scenarios is sufficient to reproduce the contact along the lobes’ longest principal axes. Implementing the full two-body problem method using finite element modeling, we numerically quantify the complex mutual interactions between Weeyo and Wenu, before the soft merger under the reported geophysical constraints and orbital configurations. All simulations demonstrate that the rotational states of both lobes become desynchronized shortly after their close approach, eventually leading to substantial misalignment along their principal axes. We also find that the lobes’ mutual gravitational torque, destabilizing their aligned orientations, is several orders of magnitude higher than gas-driven torque, suggesting that gas drag plays a negligible role in stabilizing their orientations. The present study suggests the necessity of an additional process reconfiguring Arrokoth’s shape after the merging process, possibly due to the Sky-forming impact.