Scripts remain disabled after exiting the playmode?

I have this script that disables all cameras and then leaves only one enabled. Strangely, even when exiting the playmode, the other cameras remain disabled despite the fact that they are supposed to be enabled on scene start. I then am forced to manually enable of the affected cameras. Does anyone know why?

using UnityEngine;
using System.Collections;
using System.Collections.Generic;

public class EndChase : MonoBehaviour {
	public Camera endChaseCam;
	private Camera[] allCameras;
	public Transform closestCop;
	private List<Transform> CopsList = new List<Transform>();

	// Use this for initialization
	void Start () {
		allCameras = Resources.FindObjectsOfTypeAll (typeof(Camera)) as Camera[];
		for (int i = 0; i < allCameras.Length; i++) {
  •  }*
  •  endChaseCam.gameObject.SetActive (true);*
  •  endChaseCam.enabled = true;*
  •  PoliceController[] allCops = Resources.FindObjectsOfTypeAll (typeof(PoliceController)) as PoliceController[];*
  •  for (int i = 0; i < allCops.Length; i++) {*

_ if(allCops*.gameObject.activeInHierarchy){_
_ CopsList.Add(allCops.transform);
float copDistance = (transform.position - CopsList[0].transform.position).sqrMagnitude;
closestCop = CopsList [0];
for (int i = 0; i < CopsList.Count; i++) {
float dist =(transform.position - CopsList.position).sqrMagnitude;
if(dist <= copDistance){
copDistance = dist;
closestCop = CopsList;

* // Update is called once per frame*
* void FixedUpdate () {*
* Vector3 rot = (closestCop.position - endChaseCam.transform.position);*
* if (rot != {*
* Quaternion quat = Quaternion.LookRotation (rot);*
* endChaseCam.transform.rotation = Quaternion.Lerp (endChaseCam.transform.rotation, quat, Time.fixedDeltaTime);*
* }*
* if (endChaseCam.fieldOfView > 30) {*
_ endChaseCam.fieldOfView -= 10 * Time.fixedDeltaTime;
* } else {
endChaseCam.fieldOfView = 30;

Edit: I tested this, and it appears to affect prefabs only. It appears that Unity saves the disabled state of the prefab, causing me to have to manually reactivate it. I cannot continue work on my project due to this issue. Anyone have a solution yet?

As you stated, if you manipulate prefabs directly in your script, the changes will be saved as if you did it via the inspector.
The solution is to either instantiate the prefabs and manipulate the clones or put them into the scene from the beginning.

Wow, I finally figured it out. Apparently, this line was problematic:
allCameras = Resources.FindObjectsOfTypeAll (typeof(Camera)) as Camera;

Not only would it result in the scene camera itself being disabled, but it would also cause the prefabs to keep their cameras disabled. I fixed it by changing the offending line to this:
allCameras = Camera.allCameras;

Apparently, using FindObjectsOfTypeAll causes these problems.