How would you handle this?

[JugglingReferee]

I believe that to make any ruling, you must be 100% sure of what you saw. If you're only 90% sure, you have nothing, and you should recognize that, and do better on subsequent plays.

If you're 100% sure that the ball did or did not enter the basket, and your P signals otherwise, go talk to him/her before they get to the table, or in the rare case: immediately after s/he leaves the table. Tell them what you saw and if they still insist, suggest that they consult the table crew. Alternatively, if you're the Referee on the game, and because the two officials disagree on whether the basket shall count, you can exercise Referee authority and rule that the basket counts or does not count.

On a side note, I would not ask your P if the ball went in. Instead, I would tell him what I have, and quite possibly why. By asking "if" the ball went, you are saying that you did not know. And I was taught that in 2-person, the non-calling official shall continue officiating, including knowing if the try was successful or not. Often officials will miss the gentle Team A rebound-tap that sends the ball into the hoop. The tap ensures that the basket cannot count.