but the BA report suggests that an 'amber' i.e. low level, warning, appeared on the EICAS screen about the L.E. flaps,
As I understand the report they got a amber "REV" annunctiation for one engine below V one, followed by another REV annunctiation above V one. Those are
not warning messages, as in a "Caution" or "Advisory" EICAS message, they simply appear as an indication of reverser status above the appropriate engine's EPR strip gauge at the top of the EICAS screen. In addition the Flap indication would have turned magenta since the actual flap position no longer agreed with that commanded by the Flap lever - because the LE's had in part started to retract.
Edited to add: In agreement with L337's post - these are in part the normal indications you see on the -400 landing roll. With the weight on wheels switch made, and the reversers indicating unlocked the aircraft "thought" it was in the
landing roll, so you wouldn't get any knobs bells or whistles about the config.....