Reference lists are empty?

When using some specific reference field types such as File, Metaobject and Mixed reference, ACF needs updated access to your Shopify store via special app permissions, which ACF didn't cater to in older installs. To fix it, go to the ACF dashboard and you'll see a warning message block stating the need for an update to the app's permission:

Click the button and accept the update in the following Shopify dialog.

Now your entries will be available in the reference field's dropdown in the ACF editor.