If you are able to script something real quick.
$products = Mage::getModel('catalog/product')
->getCollection()
->addAttributeToFilter('is_in_stock', 0)
->addAttributeToFilter('qty', array("gt" => 0));
Sadly I can't seem to remember how to put in the >0 in a way that is supposed to work. Maybe someone can comment on that.
What you can do with $products is run it through a foreach loop and then set the is_in_stock to the value of 1 and you should be in business.