To reproduce:
1. Create an empty project.
2. On newly created scene Add New sub scene (remember the name).
3. Save it.
4. Delete subscene.
5. Add new subscene again with the same name as in 2.
6. Dialog window appears "Rename 'SubScene' to prevent overwriting the existing Scene file.". Press Replace.

Actual result: Error appears in log "ArgumentException: A Scene already exists at 'Assets/Scenes/SampleScene/New Sub Scene.unity'."

Rename 'New Sub Scene' to prevent overwriting the existing Scene file.
Unity.Scenes.Editor.SubSceneContextMenu.ThrowIfFileExists (System.String destinationPath) (at Library/PackageCache/com.unity.entities@0.10.0-preview.6/Unity.Scenes.Editor/SubSceneContextMenu.cs:258)
Unity.Scenes.Editor.SubSceneContextMenu.CreateSubSceneAtPathAndMoveObjectsInside (UnityEngine.SceneManagement.Scene parentScene, UnityEngine.Transform targetTransform, UnityEngine.GameObject[] topLevelObjects, System.String dstPath, UnityEditor.InteractionMode interactionMode) (at Library/PackageCache/com.unity.entities@0.10.0-preview.6/Unity.Scenes.Editor/SubSceneContextMenu.cs:326)
Unity.Scenes.Editor.SubSceneContextMenu.CreateNewSubSceneAtPath (System.String path, Unity.Scenes.Editor.SubSceneContextMenu+NewSubSceneArgs args, UnityEditor.InteractionMode interactionMode) (at Library/PackageCache/com.unity.entities@0.10.0-preview.6/Unity.Scenes.Editor/SubSceneContextMenu.cs:43)
Unity.Scenes.Editor.SubSceneContextMenu.OnMenuItemForNewSubScene (System.Object userData) (at Library/PackageCache/com.unity.entities@0.10.0-preview.6/Unity.Scenes.Editor/SubSceneContextMenu.cs:189)
UnityEditor.GenericMenu.CatchMenu (System.Object userData, System.String[] options, System.Int32 selected) (at /Users/builduser/buildslave/unity/build/Editor/Mono/GUI/GenericMenu.cs:119)

Expected result:
If we strictly prohibit the replacement of the subscene file with the same name, we need to remove the dialog window on replacement of the subscene and add pre-check of the existing subscene name.