Bunch phase shift along the train due to a bunch gap transient is a concern in high-current colliders. In KEKB operation, the measured phase shift along the train agreed well with a simulation and a simple analytical form in most part of the train. However, a rapid phase change was observed at the leading part of the train, which was not predicted by the simulation or by the analytical form. In order to understand the cause of this observation, we have developed an advanced simulation, which treats the transient loading in each of the cavities of the three-cavity system of the accelerator resonantly coupled with energy storage (ARES) instead of the equivalent single cavities used in the previous simulation, operating in the accelerating mode. In this paper, we show that the new simulation reproduces the observation, and clarify that the rapid phase change at the leading part of the train is caused by a transient loading in the three-cavity system of ARES. KEKB is being upgraded to SuperKEKB, which is aiming at 40 times higher luminosity than KEKB. The gap transient in SuperKEKB is investigated using the new simulation, and the result shows that the rapid phase change at the leading part of the train is much larger due to higher beam currents. We will also present measures to mitigate possible luminosity reduction or beam performance deterioration due to the rapid phase change caused by the gap transient.