Shopify partial refund and partially refunded order is missing in Webgility.
You can apply a setting to either download open and closed orders, or override this setting in the advanced settings menu. To do this, select to download only Paid and Shipped and Paid and Unshipped orders.
1. You will need to select all options from the advance override settings, and you will need to download orders from the back date from which your order and refund are missing. To do this navigate to Integrations > Stores > Advanced Settings.
2. Next, go the Other. Then select Overwrite Shopify Order Download Settings. Choose the following, UnPaid, UnPaid And Shipped, Paid and UnShipped, Paid And Shipped.