Clear managed_file field on submit
I found a solution to this problem here: https://www.drupal.org/node/1578656

The idea is to add the following keys to the 'file_managed' field at the time you want to clear it:

$form[FORMKEY]['#file'] = FALSE;
$form[FORMKEY]['filename'] = array();
$form[FORMKEY]['#value']['fid'] = 0;


In your case it should be something like this in the form builder function:

if ( isset($form_state['storage']['reset-file-field'])
  &amp;&amp; $form_state['storage']['reset-file-field'] === true
) {
  $form['Input type']['file']['#file'] = FALSE;
  $form['Input type']['file']['filename'] = array();
  $form['Input type']['file']['#value']['fid'] = 0;

  $form_state['storage']['reset-file-field'] = false;
}


And then in your submit handler:

$form_state['storage']['reset-file-field'] = true;


The if-block is necessary to prevent the upload field being reset when you press 'upload', thus making it useless.