As for "deleting" scenes... I don't get why you would need to or want to do that... but In Axe Edit you CAN simply erase the name of the Scene.
I DO get not needing 8 (or sometimes even 4) for a given preset, and not wanting to "waste" switches on your footswitch. Here is a little tip that I do...
Make use of PER PRESET FC layouts (I'm assuming you got an FC 6 or 12 - if not... ignore this.) On my FC if one song has 4 scenes labeled INTRO, VERSE, CHORUS, SOLO, on another song I might only need 2 scenes labeled MAIN and SOLO. On that preset I set the LED rings on the unused scene switches to off and put a custom label on that switch as just a "." (It won't allow a blank - and I wish it would.) Then when I look down - I only have 2 switches lit up to choose from. On the next song, I might have 4 or even 5 again. It's per preset that way - and it gives you the same outcome at your feet as "deleting scenes".
I like my FC to be as clean and minimal as possible on stage. Only those buttons that I would need for a given song are lit up and the rest are dark. It changes a little song by song, but with custom colors it makes it super easy for me to see exactly what I need to hit with my foot for any given moment.
If you are a "guitar to amp" guy with little to no FX, or maybe only a few and prefer the stompbox world, you can setup your FC to do that too. You don't have to ever use or even see scenes. Just use a stompbox layout or a preset layout on the FC. But I'd bet a steak dinner that once you get to playing with them you will love them. They are probably the #1 feature (to me) that makes this thing so powerful and awesome.
Scenes do exactly what I used to do with a GCX switcher - turn certain FX on or off and change amp channels all with a single button press. No more tap dancing.