I have a day/night script that runs through four skyboxes, im trying to make it to where certain objects such as enemies and my flashlight be effected depending on the skybox in play.
Whatever drives your skybox transitions (probably a looping counter) should be pulled out of the skybox transition class and placed in a TimeManager class, possibly a singleton. The skybox transition script should then pull its time info from your singleton, along with anything else you want to be affected by the time of day.