Just to inform now the TK app allow to confirm the flight after schedule changes through manage bookings. The alert page shows the old and new itineraries and then you can click on "confirm new schedule/ticket", then you go to the last page with details and total cost (zero USD) and the final confirmation. Two seconds later I received the email with modified tickets.
I have a flight from CGK to Europe for next November and the IST-CGK leg departure time has been anticipated by 15 minutes from 2.35 am to 2.20 and knowing previous issues here I was ready to call TK, good to know isn't necessary anymore.