Is it possible to connect multiple Shopify stores to Zendesk Support?
The Shopify app is meant to work in a one-to-one relationship between Support and Shopify. For step-by-step installation instructions, see Integrating Shopify and Zendesk.
It is possible to install multiple instances of the Shopify app to connect multiple Shopify stores. However, keep in mind that we don't support this setup and it's not guaranteed to work.
You can either set up both instances of the app using one custom ticket field or create a separate field for each instance of the Shopify app. However, if you start to notice errors when using the app, use additional fields for the multiple installations.