Carlos Eduardo Bleck, air pilot, says in his book of memoirs [page 79] that he was the last person to shake hands with the actor Leslie Howard before Ibis of KLM/BOAC left for its last travel from Lisbon to Bristol because he was sunk by a Luftwaffe squadron over Biscaya's bay, as I wrote it in a booklet about the event.
Is the book Bleck refuses the idea that the attack was due to the wrong suspecting that Winston Churchill was aboard. The travel would be too dangerous for a prime minister, because the plain could not climb too high in case of an encounter with the Germans, was a slow one, a mere commercial line without RAF protection.
But he add a fact: the week before Captain Parmentier told him that another attack occurred to an aircraft of the "Lisbon Line", which arrived at Portela Airport in Lisbon with severe damages in the wing and fuselage.
So, if it was not the first time, there is reason enough to conclude there was not a specific motive for this action