Nubia was Christian till 13th centuryNo, it wasn't; Pharaoh was a long dead title.
Also there would be a few muslim states on the upper nile,
Ayyubid Syria, Damascus and Aleppo are still there, but no longer allied with Crusader Egypt.the kingdom might be restive or it might not be, and with the Ayyubids taken out this might prompt the far more formidable Khwarezmids to actually move in.
Once King Boniface liberates Jerusalem for Isabella and Amalric, and the pre-Hattin Frankish Oultrejordain, will he immediately press against Damascus, or take some time enjoying the fleshpots of Egypt?
In 1203, Boniface is an eligible widower, aged about 53 (and OTL went on to marry in 1204). He had one adult son, left back home as the Marquess of Montferrat. OTL, Boniface died in battle with Bulgars in 1207. If in TTL he stays at peace in Egypt, he will live past 1207.
Since Isabella and Amalric OTL died natural causes in 1205, it is not butterflied away and happens on schedule. What next? And who will Boniface have married?