Keep in the mind that the depopulated area is only the 70 mile stretch between Cairo and Beni Suef (250 to 300,000 Muslims have fled south). The elements of Egyptian society in that area that were closely aligned with the Coptic government either got wiped out or fled north when the Idwaits took over the region and have yet to move back. The Muslims of the region (95%+ of the population pre-revolt) were rural serfs and so had practically no connection with the government save through its corrupt law courts that were in the pocket of the landlords.
So there is nothing to encourage them to stay, especially when it is considered that the region is under Despotic, not Imperial control. The Coptic landlords were already nasty to their slaves serfs tenants before the slave revolt/religious war and all its attendant massacres and atrocities. The mood of their landlord cousins from the Delta coming to reclaim their relatives' lands is unlikely to have improved.
Furthermore the one force capable of keeping the Coptic landlords in line, the Roman army, is busy marching out of Egypt at maximum speed to fight in Syria. And to provision the Roman armies fighting against Iskandar Egyptian grain is going to be very useful, potentially even crucial considering that Syrian harvests have been lousy the past several years (the revolt there didn't help either). So the Romans are not in the best position to be unduly irritating the Coptic landlords.