thank you for all the replies. I have to make some corrections. I had written the original post in the first person (for simplicity) but really all this happened to my father.

Here's a more accurate account:

My father got to the luggage screening at terminal C (coming from terminal F). Before he could proceed to luggage screening, some people looked at his bp and luggage. From there he was sent to some kind of regular looking check-in desk where the luggage was weighed and he was asked to go pay EUR200 at some other payment desk. Being in a situation of extreme rush, he complied not to miss his flight. I had misunderstood and thought the luggage had been weighed and check at the gate.

I have sent an email to AF on his behalf. Let's see what they reply!