I'm not quite sure, but i don't believe there has been any further
747 flight to LPMA.
Portuguese operators (TAP, Air Luxor) have flown the Airbus 340,
Airbus 330 and Lockheed Tristar to Madeira, on special events
and on some regular/charter flights.
I don't believe that the local market is big enough for regular 747
flights.
Air Atlanta's B747 flight on the 5th of October 2002 was solely
a
PR operation by Madeira's Regional Government or ANAM (The state
company that runs both Madeira and Porto Santo aiports), to
"celebrate" the opening of the new passenger terminal.
If i recall correctly, the flight only had crew on board, both
inbound and outbound.
The event drew quite a crowd.