At the time of writing, the only place you can credit a KM Malta Airlines flight is in their own programme, KM Rewards.

To earn credits in Flying Blue - and this applies just as much to the current legal entity as it did to the predecessor airline - you would have had to have booked the flight under an AF or KL code as part of an AF or KL ticket (so, it is currently - and was only ever possible - to earn Flying Blue miles on the few routes that AF and KL used to/currently codeshare on - between MLA and CDG, ORY, LYS and AMS)