In the editor collect sources only from either the main stage or the prefab stage.

Author: turadr

Assets/Examples/Editor/NavMeshPrefabInstanceEditor.cs

@@ -2,7 +2,6 @@
 using UnityEditor;
 using UnityEngine;
 using UnityEngine.AI;
-using NavMeshBuilder = UnityEngine.AI.NavMeshBuilder;
 
 [CanEditMultipleObjects]
 [CustomEditor(typeof(NavMeshPrefabInstance))]
@@ -71,7 +70,8 @@ NavMeshData Build(NavMeshPrefabInstance instance)
         var sources = new List<NavMeshBuildSource>();
         var markups = new List<NavMeshBuildMarkup>();
 
-        NavMeshBuilder.CollectSources(root, ~0, NavMeshCollectGeometry.RenderMeshes, 0, markups, instance.gameObject.scene, sources);
+        UnityEditor.AI.NavMeshBuilder.CollectSourcesInStage(
+            root, ~0, NavMeshCollectGeometry.RenderMeshes, 0, markups, instance.gameObject.scene, sources);
         var settings = NavMesh.GetSettingsByID(0);
         var bounds = new Bounds(Vector3.zero, 1000.0f * Vector3.one);
         var navmesh = NavMeshBuilder.BuildNavMeshData(settings, sources, bounds, root.position, root.rotation);

Assets/NavMeshComponents/Scripts/NavMeshSurface.cs

@@ -299,20 +299,45 @@ List<NavMeshBuildSource> CollectSources()
                 markups.Add(markup);
             }
 
-            var scene = gameObject.scene;
-            if (m_CollectObjects == CollectObjects.All)
-            {
-                NavMeshBuilder.CollectSources(null, m_LayerMask, m_UseGeometry, m_DefaultArea, markups, scene, sources);
-            }
-            else if (m_CollectObjects == CollectObjects.Children)
+#if UNITY_EDITOR
+            if (!EditorApplication.isPlaying)
             {
-                NavMeshBuilder.CollectSources(transform, m_LayerMask, m_UseGeometry, m_DefaultArea, markups, scene, sources);
+                if (m_CollectObjects == CollectObjects.All)
+                {
+                    UnityEditor.AI.NavMeshBuilder.CollectSourcesInStage(
+                        null, m_LayerMask, m_UseGeometry, m_DefaultArea, markups, gameObject.scene, sources);
+                }
+                else if (m_CollectObjects == CollectObjects.Children)
+                {
+                    UnityEditor.AI.NavMeshBuilder.CollectSourcesInStage(
+                        transform, m_LayerMask, m_UseGeometry, m_DefaultArea, markups, gameObject.scene, sources);
+                }
+                else if (m_CollectObjects == CollectObjects.Volume)
+                {
+                    Matrix4x4 localToWorld = Matrix4x4.TRS(transform.position, transform.rotation, Vector3.one);
+                    var worldBounds = GetWorldBounds(localToWorld, new Bounds(m_Center, m_Size));
+
+                    UnityEditor.AI.NavMeshBuilder.CollectSourcesInStage(
+                        worldBounds, m_LayerMask, m_UseGeometry, m_DefaultArea, markups, gameObject.scene, sources);
+                }
             }
-            else if (m_CollectObjects == CollectObjects.Volume)
+            else
+#endif
             {
-                Matrix4x4 localToWorld = Matrix4x4.TRS(transform.position, transform.rotation, Vector3.one);
-                var worldBounds = GetWorldBounds(localToWorld, new Bounds(m_Center, m_Size));
-                NavMeshBuilder.CollectSources(worldBounds, m_LayerMask, m_UseGeometry, m_DefaultArea, markups, scene, sources);
+                if (m_CollectObjects == CollectObjects.All)
+                {
+                    NavMeshBuilder.CollectSources(null, m_LayerMask, m_UseGeometry, m_DefaultArea, markups, sources);
+                }
+                else if (m_CollectObjects == CollectObjects.Children)
+                {
+                    NavMeshBuilder.CollectSources(transform, m_LayerMask, m_UseGeometry, m_DefaultArea, markups, sources);
+                }
+                else if (m_CollectObjects == CollectObjects.Volume)
+                {
+                    Matrix4x4 localToWorld = Matrix4x4.TRS(transform.position, transform.rotation, Vector3.one);
+                    var worldBounds = GetWorldBounds(localToWorld, new Bounds(m_Center, m_Size));
+                    NavMeshBuilder.CollectSources(worldBounds, m_LayerMask, m_UseGeometry, m_DefaultArea, markups, sources);
+                }
             }
 
             if (m_IgnoreNavMeshAgent)