Fe5GeTe2 is a van der Waals ferromagnet and a topological material with partially occupied Fe sites. The topological state can be tuned via slowing cooling vs. quenching at 550 K, due to the disordered vs. ordered arrangement of the Fe atom. We propose to use X-ray photon correlation spectroscopy for understanding the ion dynamics across the two different cooling processes. The knowledge obtained can be used to guide new means for controlling the phase transition and the topological states in applications and devices.