Right click any level in the Levels tab and select “Remove Selected”.
Keep in mind, though, that the sublevel hierarchy exists in the currently opened level only - it doesn’t affect the sublevels themselves (if you want to use those without the current root level).
Example - you start out with LevelA that has LevelB and LevelC as sublevels. Then you create a new level, LevelD and make A-C sublevels of that new level.
The first setup will not be invalidated, it will just not be relevant while in LevelD.
You can go back to LevelA anytime, and it will still have B and C as sublevels.
A “persistent level” is always the topmost level, i.e. the one you open in Editor or have active in game (Start Map or anything opened with Open Level).
One thought about that - in your minimal test setup, either disable World Composition temporarily or make sure the sublevels are assigned to a layer in World Composition that has “Streaming Distance” disabled.
Also, add a print string to Begin Play of the sublevels and check if the levels get loaded in your setup (even with LSS Autoplay disabled). One possibility is that World Composition is already loading your levels.
You’re very much welcome.