Carlos Eduardo Bleck, Portuguese air pilot, stated in his book of memoirs [published in 1962, 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, during which it would be sunk by a Luftwaffe squadron over the Bay of Biscay, as I wrote in a booklet about the event.
In the book, Bleck refuses the idea that the attack was due to the wrong suspicion that Winston Churchill was aboard. The travel would have been too dangerous for a prime minister because the plane could not climb too high in case of an encounter with the Germans, and it was a slow one, a mere commercial line without RAF protection.
But he added a fact: the week before, Captain Parmentier had told him of another attack on an aircraft of the “Lisbon Line”, which had arrived at Portela Airport in Lisbon with severe damage to the wing and fuselage.
So, if the attack on the Ibis of KLM/BOAC was not the first one, there is reason enough to conclude that there was not a specific motive for such action.