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