fix

Went through to re-assign scene assets to some of the SceneRegistration assets that were older versions that had lost their entries (the scenes remained in the build settings but this needed to be updated anyway).
SceneRegistraitonEditor needed to make sure the entries list was allocated before trying to assign anything.
Adding or already having assigned the same SceneAsset that also references the SceneRegistration could cause the primary scene asset (i.e. one that has the NetworkManager instance that references it) do be deleted from the list.  This fixes that issue.

com.unity.multiplayer.mlapi/Editor/SceneRegistrationEditor.cs

@@ -112,7 +112,12 @@ private void AddEntry(ReorderableList list)
             var newSceneEntry = new SceneEntry();
             newSceneEntry.IncludeInBuild = true;
             newSceneEntry.AddedToList();
+            if(m_SceneRegistration.SceneRegistrations == null)
+            {
+                m_SceneRegistration.SceneRegistrations = new List<SceneEntry>();
+            }
             m_SceneRegistration.SceneRegistrations.Add(newSceneEntry);
+            m_SceneRegistration.ValidateBuildSettingsScenes();
         }
 
 
@@ -131,6 +136,8 @@ private void RemoveEntry(ReorderableList list)
                 m_SceneRegistration.SceneRegistrations.Remove(sceneEntry);
 
             }
+
+            m_SceneRegistration.ValidateBuildSettingsScenes();
         }
     }
 }

com.unity.multiplayer.mlapi/Runtime/SceneManagement/SceneRegistration.cs

@@ -200,6 +200,12 @@ internal void ValidateBuildSettingsScenes()
                     }
                 }
             }
+
+            if(NetworkManagerScene != null)
+            {
+                AddOrRemoveSceneAsset(NetworkManagerScene, true);
+            }
+
         }
 
         /// <summary>

testproject/Assets/Samples/EnableDisableNetworkObject/EnableDisableSceneRegistration.asset

@@ -12,11 +12,13 @@ MonoBehaviour:
   m_Script: {fileID: 11500000, guid: 180fe42d996da264ab3d32e3fc9033ca, type: 3}
   m_Name: EnableDisableSceneRegistration
   m_EditorClassIdentifier: 
-  m_SceneRegistrations:
-  - Scene: {fileID: 102900000, guid: 619b9eba5892d5a4e9dd1d6cafb0059a, type: 3}
-    IncludeInBuild: 1
-    AdditiveSceneGroup: {fileID: 0}
-    m_KnownAdditiveSceneGroup: {fileID: 0}
+  SceneRegistrations:
+  - IncludeInBuild: 1
+    Scene: {fileID: 102900000, guid: 619b9eba5892d5a4e9dd1d6cafb0059a, type: 3}
     SceneEntryName: EnableDisableSceneNetworkObject
-  m_NetworkManagerScene: 
-  NetworkManagerScene: {fileID: 0}
+    KnownAdditiveSceneGroup: {fileID: 0}
+    AdditiveSceneGroup: {fileID: 0}
+  m_NetworkManagerScene: EnableDisableSceneNetworkObject
+  m_KnownSceneRegistrations: []
+  NetworkManagerScene: {fileID: 102900000, guid: 619b9eba5892d5a4e9dd1d6cafb0059a,
+    type: 3}

testproject/Assets/Samples/SceneRegistration/AdditiveSceneGroup1.asset

@@ -12,8 +12,10 @@ MonoBehaviour:
   m_Script: {fileID: 11500000, guid: b9f97901b434bd84bb2a433719183485, type: 3}
   m_Name: AdditiveSceneGroup1
   m_EditorClassIdentifier: 
-  m_AdditiveSceneGroups: []
-  m_KnownAdditiveSceneGroups: []
+  m_AdditiveSceneGroups:
+  - {fileID: 11400000, guid: 6ad30cb0c1be4f44ba9b86d536988a50, type: 2}
+  m_KnownAdditiveSceneGroups:
+  - {fileID: 0}
   m_AdditiveScenes:
   - IncludeInBuild: 1
     Scene: {fileID: 102900000, guid: 466e828eb554ee44c900882db6c9d3a7, type: 3}

testproject/Assets/Samples/SceneRegistration/AdditiveSceneGroup2.asset

@@ -14,4 +14,13 @@ MonoBehaviour:
   m_EditorClassIdentifier: 
   m_AdditiveSceneGroups: []
   m_KnownAdditiveSceneGroups: []
-  m_AdditiveScenes: []
+  m_AdditiveScenes:
+  - IncludeInBuild: 1
+    Scene: {fileID: 102900000, guid: b12634a7636aba845801ca83d4ba61c2, type: 3}
+    SceneEntryName: AdditiveScene 4
+  - IncludeInBuild: 1
+    Scene: {fileID: 102900000, guid: 9904940443bdd09489233649a5b6e0b8, type: 3}
+    SceneEntryName: AdditiveScene 5
+  - IncludeInBuild: 1
+    Scene: {fileID: 102900000, guid: 2fc7efd990522b74caaa4cc1b42dfdc5, type: 3}
+    SceneEntryName: AdditiveScene 6

testproject/Assets/Samples/SceneRegistration/SceneRegistration.asset

@@ -12,8 +12,25 @@ MonoBehaviour:
   m_Script: {fileID: 11500000, guid: 180fe42d996da264ab3d32e3fc9033ca, type: 3}
   m_Name: SceneRegistration
   m_EditorClassIdentifier: 
-  SceneRegistrations: []
-  m_NetworkManagerScene: 
+  SceneRegistrations:
+  - IncludeInBuild: 1
+    Scene: {fileID: 102900000, guid: 228aa7771c79e6341a8fa9bc684c5766, type: 3}
+    SceneEntryName: SceneLevel-1
+    KnownAdditiveSceneGroup: {fileID: 11400000, guid: 863734e265d8f81478833cbf1902f460,
+      type: 2}
+    AdditiveSceneGroup: {fileID: 11400000, guid: 863734e265d8f81478833cbf1902f460,
+      type: 2}
+  - IncludeInBuild: 1
+    Scene: {fileID: 102900000, guid: 5add0389cebf7fa438efb6c2ac0a6fe1, type: 3}
+    SceneEntryName: SceneLevel-2
+    KnownAdditiveSceneGroup: {fileID: 0}
+    AdditiveSceneGroup: {fileID: 0}
+  - IncludeInBuild: 1
+    Scene: {fileID: 102900000, guid: 45a35678967fd6744bae54a375eec459, type: 3}
+    SceneEntryName: SceneLevel-3
+    KnownAdditiveSceneGroup: {fileID: 0}
+    AdditiveSceneGroup: {fileID: 0}
+  m_NetworkManagerScene: TestScene
   m_KnownSceneRegistrations:
   - IncludeInBuild: 1
     Scene: {fileID: 102900000, guid: 228aa7771c79e6341a8fa9bc684c5766, type: 3}
@@ -25,4 +42,5 @@ MonoBehaviour:
     SceneEntryName: SceneLevel-1
     KnownAdditiveSceneGroup: {fileID: 0}
     AdditiveSceneGroup: {fileID: 0}
-  NetworkManagerScene: {fileID: 0}
+  NetworkManagerScene: {fileID: 102900000, guid: e729f848287dcb94c99ff859aefc8511,
+    type: 3}

testproject/Assets/Samples/SceneRegistration/TestScene.unity

@@ -184,7 +184,8 @@ MonoBehaviour:
   NetworkConfig:
     ProtocolVersion: 0
     NetworkTransport: {fileID: 97227792}
-    SceneRegistration: {fileID: 0}
+    SceneRegistration: {fileID: 11400000, guid: ea4a0987e5ce32244af3b8e7699fc223,
+      type: 2}
     RegisteredScenes:
     - TestScene
     AllowRuntimeSceneChanges: 0
@@ -210,7 +211,8 @@ MonoBehaviour:
     EnableMessageBuffering: 1
     MessageBufferTimeout: 20
     EnableNetworkLogs: 1
-  m_SceneRegistration: {fileID: 0}
+  m_SceneRegistration: {fileID: 11400000, guid: ea4a0987e5ce32244af3b8e7699fc223,
+    type: 2}
 --- !u!4 &97227794
 Transform:
   m_ObjectHideFlags: 0

testproject/Assets/Scenes/SampleSceneRegistration.asset

@@ -12,12 +12,13 @@ MonoBehaviour:
   m_Script: {fileID: 11500000, guid: 180fe42d996da264ab3d32e3fc9033ca, type: 3}
   m_Name: SampleSceneRegistration
   m_EditorClassIdentifier: 
-  m_SceneRegistrations:
-  - Scene: {fileID: 102900000, guid: 9fc0d4010bbf28b4594072e72b8655ab, type: 3}
-    IncludeInBuild: 1
-    AdditiveSceneGroup: {fileID: 0}
-    m_KnownAdditiveSceneGroup: {fileID: 0}
+  SceneRegistrations:
+  - IncludeInBuild: 1
+    Scene: {fileID: 102900000, guid: 9fc0d4010bbf28b4594072e72b8655ab, type: 3}
     SceneEntryName: SampleScene
+    KnownAdditiveSceneGroup: {fileID: 0}
+    AdditiveSceneGroup: {fileID: 0}
   m_NetworkManagerScene: SampleScene
+  m_KnownSceneRegistrations: []
   NetworkManagerScene: {fileID: 102900000, guid: 9fc0d4010bbf28b4594072e72b8655ab,
     type: 3}

testproject/Assets/Tests/Manual/ConnectionApproval/ConnectionApprovalSceneRegistration.asset

@@ -12,12 +12,13 @@ MonoBehaviour:
   m_Script: {fileID: 11500000, guid: 180fe42d996da264ab3d32e3fc9033ca, type: 3}
   m_Name: ConnectionApprovalSceneRegistration
   m_EditorClassIdentifier: 
-  m_SceneRegistrations:
-  - Scene: {fileID: 102900000, guid: dd570b5916593cb41bab8beb1c9d9315, type: 3}
-    IncludeInBuild: 1
+  SceneRegistrations:
+  - IncludeInBuild: 1
+    Scene: {fileID: 102900000, guid: dd570b5916593cb41bab8beb1c9d9315, type: 3}
     SceneEntryName: ConnectionApprovalTest
-    m_KnownAdditiveSceneGroup: {fileID: 0}
+    KnownAdditiveSceneGroup: {fileID: 0}
     AdditiveSceneGroup: {fileID: 0}
   m_NetworkManagerScene: ConnectionApprovalTest
+  m_KnownSceneRegistrations: []
   NetworkManagerScene: {fileID: 102900000, guid: dd570b5916593cb41bab8beb1c9d9315,
     type: 3}

testproject/Assets/Tests/Manual/NetworkSceneManagerCallbacks/NetworkSceneManagerCallbacksSceneRegistration.asset

@@ -12,17 +12,13 @@ MonoBehaviour:
   m_Script: {fileID: 11500000, guid: 180fe42d996da264ab3d32e3fc9033ca, type: 3}
   m_Name: NetworkSceneManagerCallbacksSceneRegistration
   m_EditorClassIdentifier: 
-  m_SceneRegistrations:
-  - Scene: {fileID: 102900000, guid: 073bd2111475c0643be45b7abe6a97ad, type: 3}
-    IncludeInBuild: 1
-    m_KnownAdditiveSceneGroup: {fileID: 0}
-    AdditiveSceneGroup: {fileID: 0}
-    SceneEntryName: SceneWeAreSwitchingFrom
-  - Scene: {fileID: 102900000, guid: ee4d4a69e7f79bc4c861cd9a4b99dd0f, type: 3}
-    IncludeInBuild: 1
-    m_KnownAdditiveSceneGroup: {fileID: 0}
-    AdditiveSceneGroup: {fileID: 0}
+  SceneRegistrations:
+  - IncludeInBuild: 1
+    Scene: {fileID: 102900000, guid: ee4d4a69e7f79bc4c861cd9a4b99dd0f, type: 3}
     SceneEntryName: SceneWeAreSwitchingTo
+    KnownAdditiveSceneGroup: {fileID: 0}
+    AdditiveSceneGroup: {fileID: 0}
   m_NetworkManagerScene: SceneWeAreSwitchingFrom
+  m_KnownSceneRegistrations: []
   NetworkManagerScene: {fileID: 102900000, guid: 073bd2111475c0643be45b7abe6a97ad,
     type: 3}

testproject/Assets/Tests/Manual/RpcTesting/RpcSceneRegistration.asset

@@ -12,12 +12,13 @@ MonoBehaviour:
   m_Script: {fileID: 11500000, guid: 180fe42d996da264ab3d32e3fc9033ca, type: 3}
   m_Name: RpcSceneRegistration
   m_EditorClassIdentifier: 
-  m_SceneRegistrations:
-  - Scene: {fileID: 102900000, guid: 931469794d88a874998f1d5edd265522, type: 3}
-    IncludeInBuild: 1
-    AdditiveSceneGroup: {fileID: 0}
-    m_KnownAdditiveSceneGroup: {fileID: 0}
+  SceneRegistrations:
+  - IncludeInBuild: 1
+    Scene: {fileID: 102900000, guid: 931469794d88a874998f1d5edd265522, type: 3}
     SceneEntryName: RpcTesting
+    KnownAdditiveSceneGroup: {fileID: 0}
+    AdditiveSceneGroup: {fileID: 0}
   m_NetworkManagerScene: RpcTesting
+  m_KnownSceneRegistrations: []
   NetworkManagerScene: {fileID: 102900000, guid: 931469794d88a874998f1d5edd265522,
     type: 3}

testproject/Assets/Tests/Manual/SceneTransitioning/SceneTransitioningRegistration.asset

@@ -12,22 +12,18 @@ MonoBehaviour:
   m_Script: {fileID: 11500000, guid: 180fe42d996da264ab3d32e3fc9033ca, type: 3}
   m_Name: SceneTransitioningRegistration
   m_EditorClassIdentifier: 
-  m_SceneRegistrations:
-  - Scene: {fileID: 102900000, guid: 1c2375a896b2e8c4a841aa61224b8494, type: 3}
-    IncludeInBuild: 1
-    SceneEntryName: SceneTransitioningTest
-    m_KnownAdditiveSceneGroup: {fileID: 0}
-    AdditiveSceneGroup: {fileID: 0}
-  - Scene: {fileID: 102900000, guid: 79c2bf7d6b7a06a42a94982aaf1904d8, type: 3}
-    IncludeInBuild: 1
+  SceneRegistrations:
+  - IncludeInBuild: 1
+    Scene: {fileID: 102900000, guid: 79c2bf7d6b7a06a42a94982aaf1904d8, type: 3}
     SceneEntryName: SecondSceneToLoad
-    m_KnownAdditiveSceneGroup: {fileID: 0}
+    KnownAdditiveSceneGroup: {fileID: 0}
     AdditiveSceneGroup: {fileID: 0}
-  - Scene: {fileID: 102900000, guid: 637ab8340e96a2949adfe5bfdd42b924, type: 3}
-    IncludeInBuild: 1
+  - IncludeInBuild: 1
+    Scene: {fileID: 102900000, guid: 637ab8340e96a2949adfe5bfdd42b924, type: 3}
     SceneEntryName: ThirdSceneToLoad
-    m_KnownAdditiveSceneGroup: {fileID: 0}
+    KnownAdditiveSceneGroup: {fileID: 0}
     AdditiveSceneGroup: {fileID: 0}
   m_NetworkManagerScene: SceneTransitioningTest
+  m_KnownSceneRegistrations: []
   NetworkManagerScene: {fileID: 102900000, guid: 1c2375a896b2e8c4a841aa61224b8494,
     type: 3}

testproject/ProjectSettings/EditorBuildSettings.asset

@@ -8,9 +8,42 @@ EditorBuildSettings:
   - enabled: 1
     path: Assets/MainMenu.unity
     guid: 21c7fd68cda9dd9488fc0cc01f885e39
+  - enabled: 1
+    path: Assets/Samples/EnableDisableNetworkObject/EnableDisableSceneNetworkObject.unity
+    guid: 619b9eba5892d5a4e9dd1d6cafb0059a
   - enabled: 1
     path: Assets/Samples/SamplesMenu.unity
     guid: 037562c9b1a469f498dfb34256ddf86f
+  - enabled: 1
+    path: Assets/Samples/SceneRegistration/AdditiveScenes/AdditiveScene 1.unity
+    guid: 466e828eb554ee44c900882db6c9d3a7
+  - enabled: 1
+    path: Assets/Samples/SceneRegistration/AdditiveScenes/AdditiveScene 2.unity
+    guid: ddb4e18dbd30daf4ab011d3232a63786
+  - enabled: 1
+    path: Assets/Samples/SceneRegistration/AdditiveScenes/AdditiveScene 3.unity
+    guid: c4ebb19d1542fdb4a8fe49b774ab16a0
+  - enabled: 1
+    path: Assets/Samples/SceneRegistration/AdditiveScenes/AdditiveScene 4.unity
+    guid: b12634a7636aba845801ca83d4ba61c2
+  - enabled: 1
+    path: Assets/Samples/SceneRegistration/AdditiveScenes/AdditiveScene 5.unity
+    guid: 9904940443bdd09489233649a5b6e0b8
+  - enabled: 1
+    path: Assets/Samples/SceneRegistration/AdditiveScenes/AdditiveScene 6.unity
+    guid: 2fc7efd990522b74caaa4cc1b42dfdc5
+  - enabled: 1
+    path: Assets/Samples/SceneRegistration/SceneLevel-1.unity
+    guid: 228aa7771c79e6341a8fa9bc684c5766
+  - enabled: 1
+    path: Assets/Samples/SceneRegistration/SceneLevel-2.unity
+    guid: 5add0389cebf7fa438efb6c2ac0a6fe1
+  - enabled: 1
+    path: Assets/Samples/SceneRegistration/SceneLevel-3.unity
+    guid: 45a35678967fd6744bae54a375eec459
+  - enabled: 1
+    path: Assets/Samples/SceneRegistration/TestScene.unity
+    guid: e729f848287dcb94c99ff859aefc8511
   - enabled: 1
     path: Assets/Scenes/SampleScene.unity
     guid: 9fc0d4010bbf28b4594072e72b8655ab