Neither the app nor the boarding pass shows you whether a flight is eligible for earning Flying Blue miles. They show you valid bookings and boarding passes - they state nothing regarding whether and if you will earn miles or XPs. Just because a booking/boarding pass shows up on the app, or just because you can generate a boarding pass using either the KLM or AF apps, does not mean you are guaranteed to earn miles or XPs.

(If the flight was booked with an AF or KL flight number, rather than as a UX flight number, it would earn miles and XPs)

Unfortunately, the days of being able to "rely" on a business class flight earning miles is no more. And not only in Flying Blue - it's a feature of many programmes now, particularly in Star Alliance!

To be sure of earning miles, and if you are not booking flights with AF or KL flight codes (which are always guaranteed to earn miles and XPs, regardless of who actually operates the flight), you need to know what fare basis each sector is booking into - which is not always easy to verify, depending on the manner you choose to book the ticket - and then check the earning table which for Flying Blue earnings on UX is here. Non-listed fare bases do not earn any miles.

That "O" business class fares on Air Europa don't earn on Flying Blue has been known for some time: Air Europa - O Class

"O" business class fares on Air Europa earn nothing in any Skyteam programme except for Air Europa's own "Suma" programme