I moved your posts and the replies to a new thread in the client dev section so that we can discuss without mixing things up with the older thread.
Can you provide more information about your ACME client? Is it something custom written or are you using an existing library/client?
I’m not sure I understand the problem. It sounds like the authorization is
"status": "valid" by way of one of its challenges. The other two challenges will remain pending forever and do not need to be interacted with. Your client code should consider its job done for the authz identifier when the status of the authorization is valid.
After Jan 2nd, 2020 the API won’t return the two pending challenges you see when you poll the valid authorization.