I think you will be charged the difference in EGP and that will then be converted to USD if you are not paying in EGP cash for example. A refund will be for the original USD amount and not for the EGP amount; no arbitraging the exchange rate, I'm afraid (at least this was the case with refunds that I have done in the past). I have no idea if TA issued tickets are different, these are for airline issued tickets (both AA and other airlines have been the same). I suppose you can always get it refunded in Cairo in EGP but then you have exchange controls to deal with (impossible to take the money out of Egypt, so this is a good idea only if you have EGP denominated expenditures coming up soon). Really not worth it for a 7% movement, particularly for a volatile currency like EGP, it is one bomb blast away from a 50% exchange rate movement.

While the fare hasn't changed, taxes and fuel surcharges have gone up, maybe a lot (depends on your routing and airline used); wouldn't be surprised that it is several hundred dollars additional now.