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You can use or analyse code of below free module to change attribute set of a product :

http://www.magentocommerce.com/magento-connect/flagbit-change-attribute-set.html

The code I found from module which can change attribute set :
This code is located in /app/code/community/Flagbit/ChangeAttributeSet/controllers/Adminhtml/Catalog/ProductController.php

foreach ($productIds as $productId) {
    $product = Mage::getSingleton('catalog/product')
           ->unsetData()
           ->setStoreId($storeId)
           ->load($productId)
           ->setAttributeSetId($attributeSetId)
           ->setIsMassupdate(true)
           ->save();
}

You should pass below to this code :

• product ids ($productIds)
• store id ($storeId)
• attribute set id ($attributeSetId)