You can just start it from scratch and add the components whenever you finally want to edit it. You don't need all the yml files in the folder. Luna Engine will still work :)
It works for every other scene, but SceneBattle seems to be an exception, because when I start a battle I get this error:
TypeError: Cannot read property 'offset' of undefined
at Window_EnemyVisualSelect.e.updateWindowPosition (js/plugins/LunaEngine.js:14)
at Window_EnemyVisualSelect.updateWindowAspects (js/plugins/YEP_BattleEngineCore.js:5160)
at Window_EnemyVisualSelect.update (js/plugins/YEP_BattleEngineCore.js:5154)
at rpg_core.js:4068
at Array.forEach (<anonymous>)
at e.Sprite.update (rpg_core.js:4066)
at e.Sprite.update (js/plugins/Olivia_HorrorEffects.js:983)
at e.value (js/plugins/LunaEngine.js:14)
at rpg_scenes.js:262
at Array.forEach (<anonymous>)