Hi @byte,
If the current behaviour is affecting your issuance process it indicates a bug with the way your ACME client is polling resources. I recommend you contact the developers of the client for that.
The change to stop returning the pending challenges from a valid/invalid authorization will be going to production slightly later than I originally planned. Since it is a user-visible API change we decided to make an API announcement for it: ACME v1/v2 - Changing "Challenges" returned for invalid/valid authorizations
We'll be making that change live in production in early Jan 2020.
Thanks,