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Most likely that this tool which you are using for refreshing your product list from distributor sets incorrect values for stock.
In you need the tool that will be correctly updating your inventory from supplier, I can offer you Automated Product Import addon and Store Manager application. Those 2 products allow you to set scheduled updates using the file from your supplier. Using the tools you will be able to set default values as “in stock” to the product right in the process of import, even if you do not have column in the file for it.
Free trial version of the applications you may download here and use free for 2 weeks -
In case, you do not want to change method you do update from distributor, you can use Store Manager application and set your products to in stock in bulk. Basically, with this application all you need to do it to filter your products which became out of stock, select them and set to “in stock” in one click.
If none of the offered is not suitable for you, let me know. Maybe our developers can provide you some SQL statement.