This plugin allows you to include CSS or JS files in specific posts and pages.
No. Only plugin core files will be overwritten.
When you delete one of your CSS or JS files with your FTP client, the plugin won't automatically remove all references to that file (in case you were simply deleting to reupload it again or some other case. It tries to preserve the calls to your files. In order to remove these calls, use the plugin's options page. Using the delete button on the plugin's options page will remove the file and all references to that file in your posts and pages.