but the BA report suggests that an 'amber' i.e. low level, warning, appeared on the EICAS screen about the L.E. flaps, and 'may not ' have been noticed
There was no low level warning on the EICAS screen about the L.E. flaps. The warning was a "Dual ‘REV’ amber EICAS message."
That caused the LE flaps to retract. That retraction was not annunciated because the aeroplane thought it was doing the correct thing...