When I click "Deploy to Production" in CloudKit, it looks like this: 
As you can see, there's two updates to indexes. But the problem is, that's not the only change I made to my schema - there's new fields on some record types. They're not showing up at all.
What's more, even if I wanted to deploy just these two index changes, the Deploy button is greyed out! What's going on? How do I convince CloudKit to recognise the changes I've made?
You need Edit and manage permissions for this iCloud Container.
Even if your account is added as an admin in the team you still need to have manage iCloud permission.