I find that when projects are first started, they can be tricky to work with, especially when you make drastic changes to content/collections/order. I find that a bit of drastic treatment has helped, or at least I think it did.
Just yesterday I was trying to get a project prepared for a demo. I wanted to remove _everything_ from the top-level so I could show the error state when you have nothing in the top-level. But my preflight apps wouldn't let go of what used to be there.
I found that I needed to force-quit the app, this was drastic enough to make the app go look for the current state of things.
(I did what I intended about articles, collections, order, cards, and layouts -- then clicked preflight. Then I force-quit the app and upon relaunch, I saw what I expected.)
I think some of this drastic action helps because when you have a really basic setup (you had only one article in the top-level) it's really hard to change views to get the update notice. Some would suggest "background/foreground the app" -- and that might do it, but I find a good old force-quit is where I go.