Hi! I'm a Shopify/FB user, too. I'm looking at the Shopify Legacy app in Facebook, and I'm planning on removing it, since it's obsolete and I've set up the new Facebook app through Shopify. I'll tell you the steps I'm taking, and I'm hoping this helps you out -
In FB's Business Integrations, Select the Shopify Legacy app - click "View and Edit" on the right hand side.
Scroll to the bottom of the pop-up page that comes up when you do this - at the bottom of this page, you should see your user ID and a clickable "Remove" /Remove this app button.
When clicked, it should pop up a window asking if you want to delete posts that Shopify legacy posted to your timeline. You can select it - I'd hope that would do the trick. If not, I'm hoping that Shopify support and/or Facebook support can help you out, as I'm just another user!
Good luck! -Yani