editor script resetting variables when play mode is triggered

Sorry to bump this, but I've been trying for almost a month with no success and I'd rather bump than start a new topic...I still have no idea why the array is losing all references to the spawned GameObjects when play mode is triggered.

Just as the topic suggests, I have a script running in the editor, which creates a number of gameObjects and then stores references to them in an array within the script.

When I run the script, the custom inspector window I made to view and edit them gets really small and the slider controls and such disappear(which normally occurs when it tries to access an out-of-bounds array index.) This persists until I exit play mode and actually run the script to create the objects again (though if I don't delete the existing ones I get duplicates.)

Is there any way to keep Unity from reloading the script and losing all the information I have stored in memory at the time?

Thanks

EDIT:

This is my entire inspector script, its a very simple prototype of what I eventually want it to look like, but I doubt that this is the issue.

 using UnityEngine;
 using System.Collections;
 using UnityEditor;
 
 [CustomEditor(typeof(HexManager))]
 public class HexInspector : Editor {
 
     int xCoordinate = 0;
     int yCoordinate = 0;
 
         
 
     public override void  OnInspectorGUI()
     {
         HexManager script=(HexManager) target;
         
 
         DrawDefaultInspector();
 
 
       
         EditorGUILayout.Space();
 
          if (script.showEditor)
         {
 
             int minX;
             //Debug.Log(script.xDimension + " " + script.yDimension);
             yCoordinate = EditorGUILayout.IntSlider("Y Coordinate", yCoordinate, 0, script.grid.GetLength(1)-1);
 
 
             minX = yCoordinate;
             //if odd numbered row, is incremented to produce correct hex coordinates
             if (minX % 2 == 1)
             {
                 minX++;
             }
 
             //converting orthagonal grid coordinates into non-orthagonal hex coordinates
             minX = 0 - (minX / 2);
 
 
             xCoordinate = EditorGUILayout.IntSlider("X Coordinate", xCoordinate, minX, script.grid.GetLength(0)-1 + minX);
 
             EditorGUILayout.Space();
             EditorGUILayout.LabelField("Node at","("+xCoordinate + "," + yCoordinate + ")");
             EditorGUILayout.Space();
 
             script.grid[xCoordinate - minX, yCoordinate].passValue = EditorGUILayout.FloatField(
                 "PassValue", script.grid[xCoordinate - minX, yCoordinate].passValue);
 
 
         } 
 
          EditorGUILayout.Space();
          EditorGUILayout.Space();
          EditorGUILayout.Space();
          EditorGUILayout.Space();
          EditorGUILayout.TextArea ("THIS OPERATION CANNOT BE UNDONE, CURRENT GRID WILL BE LOST");
 
         if (GUILayout.Button("Create Grid"))
         {
             
             script.SpawnGrid();
             xCoordinate = 0;
             yCoordinate = 0;
         }
        
     }
 }

And this is the code I use to instantiate and assign the components of the instantiated gameObjects to the array(its very sloppy, I know...I'm not worrying about optimizations until I have it working correctly.)

     while (currentX < xDimension)
 {
         GameObject temp;

         
         if (drawGrid)
         {
             temp = (GameObject)Instantiate(hex, spawnPos, transform.rotation);
             temp.transform.localScale = new Vector3(distanceBetween,distanceBetween,distanceBetween);
             temp.name = xNum.ToString() + "," + yNum.ToString();
             temp.transform.parent = this.transform;
             tempNode = temp.GetComponent<HexNode>();
             tempNode.coordinates = new Vector2(currentX, currentY);
             tempNode.myController = this;
             grid[currentX,currentY]=tempNode;



     
         }
     }

I'm still not sure why the array of hexNodes (grid[,]) is being reset each time I enter and leave play mode...I really have no idea what else to try with this, but it's really becoming a bottleneck with my production right now.