Those checkboxes are form fields only and not being persistet in the database. They show if an attributes values is going to be saved in the current store. Magento will evaluate them when saving the product. When checked magento will delete the attributes value for the current store and in the frontend will fallback to its value of the default store.
I can be wrong, but your products probably really have empty description values saved for each store other than default store in the product entity tables. Thus, you actually want to find and delete those empty product descriptions.
Search for those descriptions eg. with (adapt to your needs):
SELECT d.* FROM catalog_product_entity_text AS d
INNER JOIN eav_attribute AS a ON a.attribute_id = d.attribute_id
WHERE a.attribute_code="description" AND d.store_id > 0 AND TRIM(value) = '';