This is a problem I had when working in a client site recently. He imported products for his Magento site. Somehow, all products do not use default settings for inventory anymore. Each product has its own configuration for inventory, like below picture:
In this case, it causes some problems for his site when creating orders in back-end. It will displays this error message: "The stock item for Product is not valid."
It is easy to solve the problem. We just need to update these products to "use configure settings". But how long will it take if you have to update each product when you have some thousands. Luckily, we can use database to update all products.
Go to your phpmyadmin, look at table 'cataloginventory_stock_item'. You will need to set manage_stock = 0, and use_config_manage_stock = 1 for these items. The simple sql command for this is:
UPDATE `cataloginventory_stock_item` SET `manage_stock`=0, `use_config_manage_stock`=1 WHERE...
As you want to update for many products at one time, you should try to find out your own condition which goes after WHERE. You might use a list of product ids or join with catalog_product_entity.