OnSceneChange for Don'tDestroyOnLoad GameObjects?

Hi there Unity sages, I'm a student programmer that's currently stuck in a very weird situation.

• Don'tDestroyOnLoad
• Whenever specific scenes load(e.x Main) it's supposed to make references to gameobjects in the main scene from DDOL
• Use the functions from those Gameobjects.

What I have currently done is made a preloader Scene to instantiate my Managers to hold the references and made a script for it to get references from the main scene when the scene is loaded. I achieved that by using OnEnable and OnDisable and then doing SceneContainer.GetComponentsInChildren(true); and then sorting it all out. It was working however out of the blue it just started freaking out and stop working. The OnEnable/Disable is now being randomly called(sometimes not even being called) and on first run OnEnable/Disable happen before OnAwake in the scene. I have been frustrated because of this problem for 2 days now and i've run out of ideas. Sorry for the long read! Thanks for the help!

Notice how SceneLoadCheck is called before Awake does.

   /// <summary>
     /// 
     /// Scene Swap Interaction
     /// 
     /// Resets the required References whenever the scene changes.
     /// 
     /// 
     /// </summary>
     private void OnEnable()
     {
         SceneManager.sceneLoaded += SceneHasLoaded;
     }
 
     private void OnDisable()
     {
         SceneManager.sceneLoaded -= SceneHasLoaded;
     }
 
     void SceneHasLoaded(Scene scene, LoadSceneMode mode)
     {
         Debug.Log("Scene Load Check");
 
         Debug.Log(SceneManager.GetActiveScene().name);
 
         if (SceneManager.GetActiveScene().name == "_PreLoad")
         {
             SceneManager.SetActiveScene(SceneManager.GetSceneByName("Pre-Alpha 2.1.0"));
         }
 
         
         StartCoroutine(StartUp(scene));
 
     }

The Code in question. StartUp(scene); is where I reference my objects
EDIT: I've been running more tests and it seems that my Main scene is being loaded more than once? I did SceneManager.sceneCount and it returned 4 active scenes when it should only be 2. I don't know if this might be relevant or not but it's the only result i've had in 5 hrs