Which version of WordPress do you use ?
Does someone else have access to your ftp ?
WordPress doesn't delete the "themes" or "plugins" folders, even for an update. Those folders and default themes come by default during a fresh installation of WordPress. As the 'uploads' directory under the "wp-content" folder. The 'upgrade' folder appears when you're updating the WordPress core.
If you had a backup of your site, consider restoring it. (Files + database.) If not, you should avoid uploading your images by ftp. WordPress registers in the database the URI of your media files. So to clean things up, go to your WordPress Admin under the "Media" tab. Delete permanently all broken entries (files). Make sure your images files are not in your 'uploads' folder too. Upload all your images from the "Media" tab in the WordPress Admin. Keep the same image names, so if you have posts with those images, they will display correctly (because we have clean the database entries by deleting permanently those broken files).
As for a development tip:
- Consider using source control like Git or subversion locally for controlling your files
- Backup your wordpress files and database before playing with Admin, or changing themes and plugins, ...
For Git or subversion, you can also check for GUI software if you're not comfortable with a console or command-line tool.