Difficulty with pausing and resuming EventSystem

I am making a pause screen for my game. Since there are multiple playable scene's I thought of having a pause scene and load it additive then and unload it, instead of prefabbing a canvas and instantiating every time.

Now some scene's have already have an Event System, so I disabled previous scene event system and enable when Pause scene unloads.

But the problem is that when I disable the event system script, the current input module gets set to none and remains that way even after being enabled.

Here's is part of Level Manger script responsible for loading Pause Scene (unload is handled from Pause Scene itself)

 private void Start()
     {
         if (FindObjectOfType<EventSystem>() != null){
             eventExists = true;
             es = FindObjectOfType<EventSystem>();
         }
     }
 
     private void Update(){
         if (Input.GetKeyDown(KeyCode.Escape) && !onPause) {             
             if (eventExists){
                 es.enabled = false;
             }
             SceneManager.LoadSceneAsync![alt text][1]("Pause", LoadSceneMode.Additive);
             StartCoroutine(SetActive(SceneManager.GetSceneByName("Pause")));
             Time.timeScale = 0;
             onPause = !onPause;                                  //onPause is a public static bool
         }
         if (!onPause && Time.timeScale == 0){
             if (eventExists) {
                 es.enabled = true;
                 Debug.Log("enabling event system");
             }
             Time.timeScale = 1;
         }
     }
 
     public IEnumerator SetActive(Scene scene){
         int i = 0;
         while (i == 0){
             i++;
             yield return null;
         }
         SceneManager.SetActiveScene(scene);
         yield break;
     }

[1]: /storage/temp/104209-input-unity.png