Emissary Familiar Benefits for Chosen One Paladin not correct
 

I'm using the Chosen One Archetype for the Paladin, and it automatically adds the Emissary when it is selected.

Once I create the Familiar, assign a race and a deity, it also has the Emissary listed in the Alternate Racial Trait and Animal Archetype section of the Minion tab, and both are Green. Seems good.

But when you go to Familiar Benefits, Alertness is replaced with Divine Guidance, Share Spells is replaced with Share Will, and Deliver Touch Spells is replaced with Domain Influence. So it appears that the Emissary it is applying must be for a Cleric Archetype, not for the Paladin.

What I'd expect to see is Alertness still intact, the addition of Religious Mentor, Share Spells staying intact, and Lay on Paws added for Level 2. As well as Emissary Smite at 11, True Form at 7, etc.

Any idea how this can be reported to be fixed/updated?

The Emissary Familiar Archetype on the Archives of Nethys matches what you say you're seeing on your familiar, replacing the proper abilities. It's also what I'm seeing on a test character.

The Chosen One Paladin Archetype describes the other abilities you're saying are missing from your familiar. They're applied to the Paladin, as you can see under Special Abilities on the Paladin tab for your main character.

Unfortunately, that means you'll want to use Adjustments to fix the familiar's Knowledge (Religion) and (at level 11+) give it the Smite bonuses, if you want it to go into combat. At level 7 you'll have to change your familiar's "race" manually, just like when you take Improved Familiar. The Change Shape universal monster ability that lets it go back to its original form doesn't change your familiar's stats, which should help if you need a full combat character sheet for its original form after getting True Form.

If you haven't already, you could submit a bug report via the website for the abilities that are given to the Paladin but apply to the familiar; even if they can't be added automatically maybe LWD could add an Adjustment for them. They haven't been doing much work on PF1, though.

Hope this helps.

Thanks, this is helpful. I'll post the bug, and see if it ends up clearing in the future.