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Bill Run for a specific subscription NOT all subscriptions in an account

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Bill Run for a specific subscription NOT all subscriptions in an account

We need to bill run for specific subscriptions NOT all subscriptions in an account, especially for the end of our subscription process. We have multiple usage charges in our base product, and when a subscription is ended, because our bill run is scheduled to run daily, usage charge ($0) will get picked up and generated, as a final invoice. The issue with this is oftentimes we need to upload usages days after the subscription has been ended, but because of the $0 usage charge already generated, we are not able to upload/ overwrite usage charges. 

This is an issue as we attempt to automate the process.
Does anyone know a way to isolate a subscription that has been ended so no bill run will be picked up for these subscriptions?