Hi @lancedolan,
I think we've been here before back in April: Multiple accounts to temporarily get around new authz limit? - #6 What was the cause of the leaked authorizations back then? How did you resolve the problem?
Between your history of posts, the current pending authz problem, and the malformed request problem you're troubleshooting in the other thread I think there is mounting evidence you need to revisit your architecture.
It sounds like your needs as a large integrator are perhaps not a great fit for Certbot. Have you considered using Certbot's Python ACME module directly instead of trying to script invocations of Certbot? There are also other ACME clients that can also be used programatically as a library.
I'm not sure I understand. Why are production certificate renewals affected by the staging rate limit?
Do you have access to your Certbot logs? If you do then you can likely identify pending authorization IDs and affected domains within the log retention period. If you don't have logs you should definitely fix this with a high priority!