Persistent prefabs after exit

Hi,

I have a prefab that is copied multiple times in my scene. When I run a script it changes properties like color and other things.

When I change scene and come back they where all duplicate, so I added a singleton to the prefab, but now the problem is that it destroys all objects in de scene except one.

Another thing I noticed is that if I quit unity and come back my objects get a different ID. My question is: 1) How can I make all prefabs-objects persistent if I change scene. 2) How can I make the Ids persistent after exit.

I'm quite new to unity so I would be grateful if somebody could point me in the right direction.

Here is the code attached to the prefab:

 int hmWidth; // heightmap width
 int hmHeight; // heightmap height

 int posXInTerrain; // position of the game object in terrain width (x axis)
 int posYInTerrain; // position of the game object in terrain height (z axis)

 int size = 1; // the diameter of terrain portion that will raise under the game object
 float desiredHeight = -1; // the height we want that portion of terrain to be

 //variables for the age
 int currentYear = System.DateTime.Now.Year;
 [SerializeField]
 public int yearBuild {get;set;}
   
 // variables for the MarkovChane
 private MarkovChane markovChane;
 [SerializeField]
 public int currentState {get;set;}
 [SerializeField]
 public int probability {get;set;}
 private GameObject markovScript;

 //variables to save the object
 private string fileName;
 private string filePath;
 ManholeData manholeData;

 private static bool manholeExists;
 
 
 
 //public variables in inspector
 [Header("General")]
 public int ID;
 public Terrain Terrain;
 public Text year;
 public int infrastrInitialBuild;

 [Header("Finance")]
 public float valueNew;
 public float replacementCosts;
 public int replacementDisruption;
 public float inspectionCosts;
 public int inspectionDisruption;
 public int streetDamage;

 [Header("Health")]
 public Image healthBar;
 public Text probabPerc;
 public Color[] healtColor = new Color[5];

 [Header("Death Effects")]
 public GameObject explosionEffect;
 public float blastRadius = 5f;
 public float explosionForce = 700f;
 public GameObject destroyedObject;
 public Transform smokeEffect;

 private void Awake()
 {
     ID = gameObject.GetInstanceID();
     markovChane = FindObjectOfType<MarkovChane>();
     fileName = "/" + ID + "Data.json";
     filePath = Application.persistentDataPath + fileName;

     if(!manholeExists)
     {
         manholeExists=true;
         DontDestroyOnLoad(gameObject);
     }
     else
     {
         Destroy(gameObject);
     }
     if(manholeData == null)
     {
         manholeData = new ManholeData();
     }
 }
 
 void Start()
 {
   
     
     if (!File.Exists(filePath))
     {
     //calculates a random build-year ans pass it to the MarkovChane
     yearBuild = Random.Range(infrastrInitialBuild, currentYear);
     year.text = yearBuild.ToString();
     markovChane.Age(yearBuild);

     //saveGameData
     manholeData.savedID = ID;
     manholeData.savedState = currentState;
     manholeData.savedProb = probability;
     manholeData.savedYearBuild = yearBuild;

     string json = JsonUtility.ToJson(manholeData);
     File.Create(filePath).Dispose();
     File.WriteAllText(filePath,json);

    // Terrain = Terrain.activeTerrain;
     hmWidth = Terrain.terrainData.heightmapWidth;
     hmHeight = Terrain.terrainData.heightmapHeight;
     }
     else
     {
         string json;
         json = File.ReadAllText(filePath);
         manholeData = JsonUtility.FromJson<ManholeData>(json);

         currentState =    manholeData.savedState;
         probability = manholeData.savedProb;
         yearBuild = manholeData.savedYearBuild;

         healthBar.color = healtColor[currentState];
         probabPerc.text = probability.ToString() + "%";
         year.text = yearBuild.ToString();

     }
     
 }

 
 void Update()
 {
 }


 public void Health(int state)
 {
     if (!File.Exists(filePath))
     {
     //gets the state back from the MarkovChane and calculates the probability that the asset is actually in given state
     currentState = state;    
     probability = Random.Range(1,100);
    
         if(probability >=75 || probability <=88 && state !=0) 
         { 
             currentState = currentState-1;   
         }
         else if(probability >= 88 && state !=5)
         { 
             currentState = currentState+1;  
         }
       
     healthBar.color = healtColor[currentState];
     probabPerc.text = probability.ToString() + "%";
     
     
     if(currentState == 4)
     {
         Explosion();
     }
     }
     
 }
  void Explosion()
 {
     //show effect
     Instantiate(explosionEffect, transform.position, transform.rotation);

     //Add Force
     Collider[] collidersToDestroy = Physics.OverlapSphere(transform.position, blastRadius);

     //Replace the GameObject with the destroyed one   
     Instantiate(destroyedObject, transform.position, transform.rotation);
     Destroy(gameObject);

     //Shatter the pieces around
     Collider[] collidersToMove = Physics.OverlapSphere(transform.position, blastRadius);
     foreach (Collider nearbyObject in collidersToMove)
     {
         Rigidbody rb = nearbyObject.GetComponent<Rigidbody>();
         if (rb != null)
         {
             rb.AddExplosionForce(explosionForce, transform.position, blastRadius);

         }
     }

     // Damage left: Crater and smoke
     // get the normalized position of this game object relative to the terrain
     Vector3 tempCoord = (transform.position - Terrain.gameObject.transform.position);
     Vector3 coord;
     coord.x = tempCoord.x / Terrain.terrainData.size.x;
     coord.y = tempCoord.y / Terrain.terrainData.size.y;
     coord.z = tempCoord.z / Terrain.terrainData.size.z;

     // get the position of the terrain heightmap where this game object is
     posXInTerrain = (int)(coord.x * hmWidth);
     posYInTerrain = (int)(coord.z * hmHeight);

     // we set an offset so that all the raising terrain is under this game object
     int offset = size / 2;

     // get the heights of the terrain under this game object
     float[,] heights = Terrain.terrainData.GetHeights(posXInTerrain - offset, posYInTerrain - offset, size, size);

     // we set each sample of the terrain in the size to the desired height
     for (int i = 0; i < size; i++)
         for (int j = 0; j < size; j++)
             heights[i, j] = desiredHeight;

     // go raising the terrain slowly
     desiredHeight += Time.deltaTime;

     // set the new height
     Terrain.terrainData.SetHeights(posXInTerrain - offset, posYInTerrain - offset, heights);

    Instantiate(smokeEffect, transform.position, transform.rotation);

 }

 [System.Serializable]
 public class ManholeData
 {
 public int savedID;
 public int savedState;
 public int savedProb;
 public int savedYearBuild;

 }