Here is my situation. Clearly, I know now that booking through the airline is what I should do next time. However, I still need help with this situation.
OTA: mytrip.com (aka airtickets24.com, fantasticgreece.com)
Jan 19- purchase 7 tickets from PSA to JNB for travel in June, received e-tickets for one total itinerary on Alitalia + EgyptAir
Jan 31- receive email from OTA that one EgyptAir leg of our flight (Cairo-JNB on June 16) has been cancelled and would we like to be put on the June 17 flight. We confirmed yes we wanted the change through email/mytrip.com/phone call but did not receive etickets as of this posting.
Jan 31, Feb 1, Feb 6 called the OTA and asked for our new etickets displaying the new flights. They have told us that they deal with tickets based on departure. Alitalia says that the tickets will be cancelled if the OTA doesn't deal with this by March 1.
Good: EgyptAir confirmation code shows the new flights with seat selections confirmed.
Bad: Alitalia(issuer of tickets) confirmation code shows that we only get to Cairo and there is no existing flight to Johannesburg. There are, however, return flights at the correct time from JNB to PSA.