diff --git a/Editor/ScenePartitionSO.cs b/Editor/ScenePartitionSO.cs
index b598ee5..aa29a49 100644
--- a/Editor/ScenePartitionSO.cs
+++ b/Editor/ScenePartitionSO.cs
@@ -163,7 +163,11 @@ public void Save()
 
                         if (match.Success)
                         {
-                            // Extract the file number
+                            // Modify scene data.
+                            // Optional: ClearRootOrderProperty.
+                            ClearRootOrderProperty(ref sceneData, i, lastIndex);
+
+                            // Extract the file number.
                             string id = match.Groups[1].Value;
 
                             // Write data to disk.
@@ -382,5 +386,47 @@ public void ClearCache()
         {
             data = null;
         }
+
+        /// <summary>
+        /// Sets the m_RootOrder property to '0' on all transforms and prefab transform modifications.
+        /// The property changes every time you add/remove something in the scene for each object underneat it in the hierarchy.
+        /// This results in a lot of changes in source control that might cause conficts, and we don't want that.
+        /// This does however change the scene hierarchy order, so if things are order dependent this will break it.
+        /// </summary>
+        private void ClearRootOrderProperty(ref string[] data, int i, int lastIndex)
+        {
+            using (new ProfilerUtility.ProfilerScope($"{nameof(ClearRootOrderProperty)}"))
+            {
+                const string prefabHeaderPattern = "--- !u!1001 &";
+                const string transformHeaderPattern = "--- !u!4 &";
+                const string prefabRootOrderPropertyPattern = "      propertyPath: m_RootOrder";
+                const string transformRootOrderPropertyPattern = "  m_RootOrder:";
+                const string numberPattern = @"[\d-]";
+
+                // If object is a Prefab.
+                if (data[i].StartsWith(prefabHeaderPattern))
+                {
+                    for (int j = i; j < lastIndex; j++)
+                    {
+                        if (!data[j].StartsWith(prefabRootOrderPropertyPattern)) continue;
+
+                        data[j + 1] = Regex.Replace(data[j + 1], numberPattern, "0");
+                        return;
+                    }
+                }
+                // If object is a Transform.
+                else if (data[i].StartsWith(transformHeaderPattern))
+                {
+                    // Reverse loop since property is usually at the bottom of the transform component.
+                    for (int j = lastIndex - 1; j >= 0; j--)
+                    {
+                        if (!data[j].StartsWith(transformRootOrderPropertyPattern)) continue;
+
+                        data[j] = Regex.Replace(data[j], numberPattern, "0");
+                        return;
+                    }
+                }
+            }
+        }
     }
 }
\ No newline at end of file