They posted an update about this on facebook a couple of days ago, so it seems they'll start mid-April:
"EGYPTAIR have the pleasure to announce the recommencement of its regular flights between Cairo and Tokyo starting from the 15th of April 2012 with its modern Boeing 777-300 aircraft, departure times and dates are as follows:
Flight number: 964 / 965
Operating days from Cairo: Sunday and Tuesday
Operating days from Tokyo: Monday and Wednesday
Departure time from Cairo: 2250 [10:50 pm ]
Departure time from Tokyo: 2120 [ 9:20 pm ]"