This reply is a little late, but maybe helpful to others.
Exporting your Shopify inventory in CSV format and setting the available quantity to zero is one way of taking stock. Keep in mind this is not a good way to take inventory unless you have shut your store and are not making any online or in-store sales.
There are a couple of stock taking apps that can do this including Shopify's own Stocky. I would recommend the "Stock Take" app for a lower cost option ($4.99/month). You can take stock or zero out your inventory in just 4 clicks. Select the inventory location, choose whole store or filter by vendors/product types, and then instead of taking stock, select update stock. This will zero out your 50,000 items in a couple of minutes.
Full disclosure: I work for BR Data Solutions the author of Stock Take.