Hope this is of use to you.
window.onbeforeunload = confirmExit;
function confirmExit()
{
return "Warning: Your file upload is in progress!!";
}
The plugin used for fileupload in this project is blueimp jquery File Upload
I've faced no upload breaking, can add the files later on in the queue. I can't really say about uploadify as i've not tried it. May be the documentation of uploadify can be a great help to you.
Please search with your error code.
http://www.uploadify.com/forums/discussion/556/another-one-on-io-error-2038/p1