Upload controls can't be given default file paths for security reasons, so when your updatepanel fires and the upload controls are refreshed, they lose the files they were previously pointing to. That is just how file uploads work, there is nothing you can do about it. Even if this did work, you can't asynchronously upload files in an update panel anyway. The other problem with update panels and external jQuery scripts is that the events you attached originally to make the scripts work now no longer work because the controls they were originally attached to have been destroyed and recreated by the update panel. To fix this you need to change how you attach the events to the controls.
http://forums.asp.net/t/1982846.aspx?How+to+run+javascript+after+updatepanel+execution+completed[
^]
Basically...don't use file upload controls inside update panels, find another way to do what you're doing.