Objects instantiated in custom editor not saving.

I have the following custom editor:

 using System.Collections;
 using System.Collections.Generic;
 using UnityEngine;
 using UnityEditor;
 
 [CustomEditor(typeof(CheckpointSystem))]
 [CanEditMultipleObjects]
 public class CheckpointPositionSelect : Editor
 {
     private GameObject newCheckpoint;
 
     void OnSceneGUI()
     {
         RaycastHit hit;
         Ray ray = HandleUtility.GUIPointToWorldRay(Event.current.mousePosition);
         if (Physics.Raycast(ray, out hit, 1000))
         {
             Handles.color = new Color(0.3f, 1f, 0.3f, 0.3f);
             Handles.CylinderHandleCap(0, new Vector3(hit.point.x, hit.point.y + 2.5f, hit.point.z), Quaternion.LookRotation(Vector3.up), 5, EventType.Repaint);
             SceneView.RepaintAll();
             if (Event.current.Equals(Event.KeyboardEvent("C")))
             { //IMPORTANT PART
                 CheckpointSystem cps = (CheckpointSystem)target;
                 Vector3 placePosition = new Vector3(hit.point.x, hit.point.y + (cps.CheckpointPrefab.transform.localScale.z / 2), hit.point.z);
                 newCheckpoint = PrefabUtility.InstantiatePrefab(cps.CheckpointPrefab as Object) as GameObject;
                 newCheckpoint.transform.position = placePosition;
                 newCheckpoint.transform.parent = cps.transform;
                 newCheckpoint.name = "Checkpoint " + cps.transform.childCount;
                 Undo.RecordObject(newCheckpoint, "Checkpoint");
             }
         }
     }
 }

When I create an object (which is referenced in CheckpointSystem) the scene/editor doesn't "recognize" it, only when I move the created object's transform the changes are indentified.