At dusk, the Jingan Army abandoned the squad hunting mode and regrouped.
The focus of the regrouping was naturally on the elite county warriors and the Divine Arm and Armored units, with other camp soldiers merely accompanying them, as they wouldn't be of much use in a real fight.
The reason the Jing'an Colonel reinstated the city guard units for defense was to prevent the Skinwalker ghosts from retaliating against his troops.
As for whether the city guard units that were swapped in would be attacked by ghosts, that was beyond his concern.