Okay, there are a few topics to respond to here, so I’ll start with the big stuff first.
Well, you can number them if you want. It’s just that Scrivener can number them for you, when you compile, so in most cases spending time numbering (and renumbering whenever you insert a chapter) is a waste of time. This is the kind of stuff that computers can do well, so you might as well take advantage of it if you can. But again, you can treat Scrivener like a “typewriter” if you want. This doesn’t need to be complicated, nor should it require you to change the way you prefer to work. The idea here is to find a comfortable way to work. If you want to number things, go right ahead.
That’s perfectly fine. An outline in Scrivener is nearly always going to evolve as the piece matures—only people who rigidly plan out every little detail before they write a word can likely say otherwise. For people that organically grow a book however, do whatever works for you in the outliner. There aren’t many rules here.
Yes, and that is all I was trying to help you with. I didn’t realise that “Bug River” was supposed to be a scene and not a chapter, so it was inadvertantly a bad example, but I’m sure you get the idea now. A chapter break can be expressed as a folder, and scene breaks as one file to the next.
Okay, again, when I suggested you move the text out of the folder, I was thinking that folder was meant to be a chapter break. However, in this case the problem is not that the folder has text, it is that this item is a folder. Right-click on the “Bug River” item in the Binder and select Convert to File. You’ll probably want to move the scenes back out that you indented, too. Note the Documents/Move/Left command can be useful for this (you can add Left/Right/Up/Down as buttons on your toolbar, too).
Have you gone through the Interactive Tutorial (help menu) yet? I consider it to be an invaluable introduction to the basics of the program.
That is not very easy to do, especially accidentally. Even if you accidentally trash part of your outline, it will merely be moved to the Trash folder in your Binder. You would have to do that, and then invoke the Project/Empty Trash… menu command, and then click through a warning message to really delete parts of your outline.
It’s also, I should say, not even theoretically possible to make a sequence of moves in the outliner that cannot be undone. Everything is reversible, even files can be converted to folders and vice versa, as you’ve witnessed.
But if you are hesitant to rip into the software and play, maybe do your experimentation and learning in the tutorial project. You can always rebuild that to its factory default by deleting it in the Finder and creating a new copy from the Help menu.