How to reproduce:
1. Create a new project
2. In the Hierarchy window, right-click > 3D Object > Cube
3. Drag the Cube from the Hierarchy window into the Project window
4. Delete the "Cube" GameObject from the Hierarchy window
5. Drag and drop the "Cube" prefab from the Project window into the Scene view
6. Press "Delete" key on the keyboard
7. Observe the Hierarchy window and the Console window

Actual result: The "Cube" GameObject is not destroyed and a warning "The operation "SoftDelete" cannot be executed because the selection is a root folder or an immutable asset." is thrown
Expected result: The "Cube" GameObject is destroyed

Reproducible with: 6000.3.0a1, 6000.3.11f1, 6000.4.0b12, 6000.5.0a8
Not reproducible with: 6000.0.70f1, 6000.2.0b2 (d4c40f50eb81)

Reproducible on: Windows 11
Not reproducible on: macOS 26.3 (M1 Max)

Workaround: Select the "Cube" GameObject in the Hierarchy window and Press "Delete" key on the keyboard

UPDATE:

This is focusing issue in which focus returns to ProjectBrowser view instead of the SceneView as it should. This is indicated by the blue "underline" in the View's tab: while dragging the GO the SceneView is focused (blue line appears under the tab) but after the drop focus switches back to the ProjectBrowser.

This means key events like Delete will go to ProjectBrowser instead of the SceneView. Clicking within the SceneView re-focuses it allowing key events to function correctly.