One reason Egypt will be uninhabitable (desolate) for forty years could be the result of nuclear warfare and the effects of the Tribulation. It is very likely that the forty-year period will stretch into the millennium. The curse on Egypt will be slowly lifted during the millennium.
“And I will make the land of Egypt a desolation in the midst of desolated countries; and her cities shall be a desolation forty years among cities that are laid waste. I will scatter the Egyptians among the nations, and disperse them among the countries” (Ezekiel 29:12).