update

Decided on a different approach to resolving this issue.

Author: NoelStephensUnity

com.unity.netcode.gameobjects/Editor/NetworkManagerHelper.cs

@@ -87,15 +87,12 @@ private static void EditorApplication_playModeStateChanged(PlayModeStateChange p
         /// </summary>
         private static void ScenesInBuildActiveSceneCheck()
         {
-            var scenesList = EditorBuildSettings.scenes.ToList();
-            var activeScene = SceneManager.GetActiveScene();
-            var isSceneInBuildSettings = scenesList.Count((c) => c.path == activeScene.path) == 1;
 #if UNITY_2023_1_OR_NEWER
             var networkManager = Object.FindFirstObjectByType<NetworkManager>();
 #else
             var networkManager = Object.FindObjectOfType<NetworkManager>();
 #endif
-            if (!isSceneInBuildSettings && networkManager != null)
+            if (!IsActiveSceneInBuildList() && networkManager != null)
             {
                 if (networkManager.NetworkConfig != null && networkManager.NetworkConfig.EnableSceneManagement)
                 {
@@ -104,20 +101,47 @@ private static void ScenesInBuildActiveSceneCheck()
                         $"to synchronize to this scene unless it is added to the scenes in build list.\n\nWould you like to add it now?",
                         "Yes", "No - Continue"))
                     {
-                        // Double double check that the EditorBuildSettings.scenes has not changed already before adding
-                        // this scene to the array (Parrel Sync issue)
-                        scenesList = EditorBuildSettings.scenes.ToList();
-                        isSceneInBuildSettings = scenesList.Count((c) => c.path == activeScene.path) == 1;
-                        if (!isSceneInBuildSettings)
+                        // Double check that the scene hasn't already been added to the scenes in build list (potential issue with Parrel Sync)
+                        if (!IsActiveSceneInBuildList())
                         {
-                            scenesList.Add(new EditorBuildSettingsScene(activeScene.path, true));
+                            var scenesList = EditorBuildSettings.scenes.ToList();
+                            scenesList.Add(new EditorBuildSettingsScene(SceneManager.GetActiveScene().path, true));
                             EditorBuildSettings.scenes = scenesList.ToArray();
                         }
                     }
                 }
             }
         }
 
+        private static bool IsActiveSceneInBuildList()
+        {
+            var scenesList = EditorBuildSettings.scenes.ToList();
+            var activeScene = SceneManager.GetActiveScene();
+            var activeSceneAsset = AssetDatabase.LoadAssetAtPath<SceneAsset>(activeScene.path);
+            var activeSceneHash = activeSceneAsset.GetHashCode();
+
+            foreach (var scene in scenesList)
+            {
+                var sceneAsset = AssetDatabase.LoadAssetAtPath<SceneAsset>(scene.path);
+                var sceneAssetHash = sceneAsset.GetHashCode();
+                if (activeSceneHash == sceneAssetHash)
+                {
+                    return true;
+                }
+                if (sceneAsset.name == activeSceneAsset.name)
+                {
+                    if (scene.path != activeScene.path)
+                    {
+                        Debug.LogError($"Active scene {activeScene.name} with path ({activeScene.path}) is potentially a duplicate of " +
+                            $"scene {sceneAsset.name} with a path of ({scene.path})! Excluding from automatically adding to the scenes in build list!");
+                        // Exit as if it did find a perfect match
+                        return true;
+                    }
+                }
+            }
+            return false;
+        }
+
         /// <summary>
         /// Invoked only when the hierarchy changes
         /// </summary>