I don't know about NetBeans, but PhpStorm has a feature that allows uploading files as soon as they change to a server (via FTP or SSH).
I don't have a lot of experience with this feature but it does seem to work well. PhpStorm can also be configured to deploy changes that occurred outside (it seems to do so as soon as it regains focus). It also seems to properly delete files that have been deleted from the project, so it's a real sync, not just "upload".
See how to configure it under "To have PhpStorm upload changed files automatically" here: http://www.jetbrains.com/phpstorm/webhelp/uploading-and-downloading-files.html