Files 404ing/when a theme is modified, all links to images and css files are broken

Hello,

I've noticed that when I change any aspect of a theme, drupal can't find images and css files. For example. I went into "Appearance/Bartik/Settings" and changed the color set to "Slate". When I save the configuration and the page reloads, the background is now entirely white and there are no images on the page. The logo is broken as well. When I go into the source code (from a browser) and pull out the url of the logo and try to visit that link, it gives me a "Not Found" error. When I go and access the files via ftp, the file exists in the same path, so why am I getting a "Not Found" error? I checked the file permissions and folder permissions and those all look fine. I've even relocated the folder where files are stored to no avail. Help would be appreciated.