Because scenes are "snapshots" of the rack at a moment in time, they cannot be edited "live". If you alter something and then re-apply the scene, those changes will be lost unless you enable Rehearsal Mode in the Options menu. Rehearsal Mode prevents inadvertent scene changes by prompting you to confirm your intent to change scenes.
Options|Rehearsal Mode is a special mode that helps you avoid losing changes to a scene before updating it. If this option is enabled, any scene change will result in this prompt. You have the opportunity here to cancel the scene change, then you can update the scene to save changes.