This is Elias from Shopify Support. I'd be happy to point you in the right direction!
In order to get a refund on third-party apps, we recommend uninstalling any of the apps you're not using first. This way, it helps the app devs confirm that you're no longer using the app, and you can start a refund request by contacting the app developers.
If the third-party app is installed through our App Store, the refund is returned to the original form of payment and the amount will be based on the approved refunds from the developers. Though the original bill is one bill, you can view your invoice on Shopify. The invoices on Shopify will show a breakdown of the app charges, so you can know how much you're expecting to get back.
That being said, if the app is installed from a developer's website, then the app charge isn't handled by Shopify. For these instances, you'll need to check with the developers directly on their refund process.
Have you heard back from the app devs yet?