Keep in mind that Lightroom uses a database to keep track of the location and names of all the items you've imported into the database (aka Catalog).
Any changes you make from within the Folders panel in Lightroom are applied directly to the files and folders on your hard drive, but the reverse is not true: If you make changes to the names or locations of files or folders outside Lightroom, you then need to right-click (or control click) on the folder and select Synchronize from the pop menu to get Lightroom's database up to date.
It's critical to keep your "physical" files/folders (those on the hard drive) up-to-date within Lightroom.
You won't be able to Develop files that Lightroom can't find (though you can make Slideshows and Web galleries with just the full size previews within Lightroom).