If everything has been working just fine until now, the likely culprit is that the Webhook from Shopify needs to be refreshed. Head over to Carts => Shopify and click the "Refresh Webhooks" button. Then, head back over to the Orders page and click on "Import Orders" to grab the ones that are missing.
If you are just getting started with Shopify + FetchApp, and orders aren't being received from Shopify it's often because payments are only being authorized rather than paid. FetchApp doesn't process orders until they are marked as paid by Shopify (unless you specify otherwise via your FetchApp settings), so that people can't access your files until after they've paid.
To automatically authorize and charge payments when an order is placed, go to the checkout and payment preference page in your Shopify account and update your settings to not only authorize, but also immediately charge orders.
A second reason that orders might not show up in FetchApp is because there is a mismatch in the SKUs. As of right now, Shopify and FetchApp don't automatically sync when a change is made in either place. Therefore, if you change the SKU in Shopify, FetchApp still has the original SKU, so they will no longer match.
Better synchronization is on the way in the near future.