Depending on how the library is packaged for the language of your choice, you may be able to upgrade without issue. The WSDLs are packaged with every version of BIG-IP and can be accessed via HTTP: https:///iControl/iControlPortal.cgi. If you're using Pycontrol or Perl, they pull the WSDLs down dynamically. If you're using Ruby or Java you'll want to update your iControl libraries as the WSDLs are packaged with the library and therefore static. Hope this helps!
As far as I know, the System.ConfigSync.download_file method has not gone away. It's still defined in the API references as was as in the .Net assembly and Java library. When you say you can't find it, where exactly are you looking? If you let me know your specifics, I'll point you in the right direction.