I am logged in as Admin. In 'Reorganize Pages', moving pages from the main navigation schema to the Trash, the item(s) still show in the main navigation on the site. In other words, moving items to the Trash has no effect. Image attached showing a page titled "Introduction" in the Trash folder. That page still shows up on the live site even after committing the change.
Since you're using apostrophe-workflow, it's most likely that you need to commit the changes to those pages for the changes to take effect in the nav (in Live mode, at least). Check out the "Workflow" menu item (at the top of the page) to do this.