404 Not Found is a standard message. It cannot find the webpage file since it was deleted. The new one has maybe a wrong path or so. I think you can safely ignore this message for now and focus on your root folder of the web host.
First check if you have deleted accidentally any of the files/folders that are put into the "WEBROOT" of your hosting by "GoDaddy." GoDaddy offers I believe two types of hosting: cPanel or Windows based. For the Windows based you should see something like;
Access Logs (folder)
db backups (folder)
hcc thumbs (folder)
aspnet client (folder)
If you believe you have all files provided by the system, for troubleshoot purpose only I would try to delete all website files manually (not through filezilla) and for the first time, upload the website files/folders once again manually. They all need to be on the root folder of your hosting space. As far as I remember, if you access your hosting account directly through web console, you have only access to your webroot folder, but through filezilla you can access other folders, thus it can happen that someone accidentally selects the wrong folder (e.g. webroot ftp or webroot public).
If the above works, you have the problem from within filezilla. Ensure your account information are correct and that your "WEBROOT" folder is correctly addressed. Remember all your website files and folders and ensure you do not delete any system folders/files of GoDaddy.
From my experience, filezilla is a great tool but can be tricky when using it the first few times.
cPanel should be about the same but there is a chance that the hosting system files are different than those listed above. I have both hosting types but cannot access cPanel right now to verify.