Squarify.io will automatically keep inventory counts between 1 Square Location and 1 Shopify Shop in sync. For example, if you sell 2 units of SKU A in Shopify, 2 units will be automatically deducted from Square, and vice versa.
I've been using squarify for the last 6 months and I am very happy with the results. I would highly recommend this to small business owners who are using square and shopify. It is affordable compared to other options on the market too.