In Jamf, you can click the "Delete" button in the bottom right-hand corner from the <Platform> App Store Apps policy. I believe that once you've purchased an app through Apple School Manager, there isn't a way to delete it completely. For one-off apps that I am no longer using, I created an additional Location and transferred all of the app licenses to that location.
Simply having an app listed in School Manager is pretty much irrelevant. (I have a bunch of apps listed there that we no longer use, as they were being used for a specific use-case that has long since gone away.) School Manager just lists all the apps that have ever been obtained, as long as they're still available through the App Store.
Similarly, having the apps listed under the VPP settings in Jamf is also irrelevant; that's just going to mirror what is listed in School Manager.
In both cases, if you're not using the app - disregard it in both places. There really isn't a way to hide or remove an app from either School Manager or the VPP settings in Jamf.
The only thing that matters is if you have the app listed under Mac/iOS App Store Apps (under Content Management in the navigation bar) and scoped for machine(s)/user(s). If the app isn't listed there, it's not being deployed through Jamf.
You can purchase it as many times as you want, it just adds on to the VPP licences you have.
Sounds like you have two of the same policies that is deploying the app. I would double check your policies and ensure you only have one.
If you only have one delete it and start again. Should do the trick.
Hope this helps
Remove an app If it is a VPP-enabled app, you will need to go to Apple's VPP portal, log in, and remove the app from there. If the app is not VPP enabled, you can simply click the ellipsis on the right side of the app and then click "Remove App" to remove it entirely from your Jamf Now instance.
Has anyone tried this?