Yes the FNC is still valid. I have the email confirmation which mentions that I reserved using the FNC. The customer service associate who raised a case for me did say that I had made the reservation correctly using the certificate but Marriott somehow charged the points instead.

I just received another email from the hotel.

”Thank you for reaching back out to Marriott Bonvoy® regarding your free night award certificate. I apologize for any confusion my wording may have caused. A certificate can be a points redemption certificate or a free night award certificate or even a gift certificate. The certificate can not be changed after you have checked into a reservation. I do show that you have two free night award certificates in your account. One will expire on 6-30-2022 and the other on 12-2-2022. If you have additional questions, please reply to this email or contact Marriott Bonvoy® Customer Care at 1-800-535-4028.”

I have asked them to provide the terms and conditions where it says that Marriott can choose to change the payment method as per their will and not honor the original reservation.
Edit: Just got another delivery failed to recipient email. It’s like Marriott intentionally wants to have a shoddy customer service