RapidWeaver doesn’t check the server for files that have been deleted or changed. RapidWeaver won’t delete files (a good thing) for you on the server either.
You can tell what pages RW will republish by the “blue” indicator by the page name.
You can also right click on a page name and republish individual pages.
You can also republish all files from the menu or by clicking the little arrow next to publish on the menu bar.