I like fix order too.
It is much more intuitive to find your Notes. So after I set a range in which I can, should or want to work on a note, I normally won’t change it anymore.
For me it is the better way to use filter in a search to get adequate overviews, than to rearrange on the Agenda.
Update: Starting from Agenda 11.2, when a project contains notes that are placed On the Agenda they receive a small orange dot to indicate this fact, making it easier to locate those projects that are currently ongoing or needing your attention most.
Unfortunately there’s no bulk action at this moment on iPad to remove more than a single note. The fastest way would be using the keyboard shortcut if you have a keyboard attached. I realise this can still take quite a bit of time. If you have access to your notes on a Mac, the fastest way is to do it there as on macOS multiple selection and bulk unmarking as On the Agenda is possible.
The trick would be to select a note, but in a way you don’t edit the text of the title or body of the note. For example by tapping at the edges of the note or in the empty area on the right side of the title before the date at the top of the note. Once you have the note selected, try ⌘ A to select all notes. You can then use ⇧⌘ U to remove the notes from On the Agenda. Let me know if this works.
Having figured out that I had the box checked that put all my notes “On the Agenda,” it strikes me that unless I am missing something I now have two manually-formed work areas, On the Agenda and Today. I don’t mind On the Agenda being the place where I manually curate what’s there and what’s not, but I’d like to be able to autopopulate Today to, for example, show me all the files I have worked on today (or even over a span of days).
I was able to select all the notes, but I hadn’t realized the keyboard shortcut — since I was already fooling with the mouse, I went for a control-click and didn’t see a command to toggle “Mark as On the Agenda” in the contextual pop-up.