I took an overnight train from Sofia (Bulgaria) to Istanbul (Turkey), but that was in 2019, so I can’t tell you for sure :)
I think you just have to make the reservation in the train station

Yes it is running again since this May. As @Louisa says you have to make the reservation locally in Istanbul in this case (e.g. Halkali, Sirkeci or Sögütlücesme station). Best to do it in Sirkeci. Ticket office should work from 8 am till 8pm. Sometimes there’s no one sitting there, so just be patient and wait until some ticket officer comes. 

In another thread someone wrote that in the opposite direction it is fully-booked for yesterday and today… so if you have the chance, book it in advance!

If Istanbul-Plovdiv is fully booked, then ask for Istanbul-Dimitrovgrad reservation and change in Dimitrovgrad to the (reservation-free) seating carriages.

Amazing thanks - yeah going in from Dimitrovgrad and been struggling to book that as well. Will just have to keep everything crossed that it isn’t fully booked by the time I reach Bulgaria. 
 

Thanks for your help

If you are before already in BG should be no problem if you book it 4-5 days before… especially if you only want until Dimitrovgrad.

Unfortunately I only get to Bulgaria about 24hours before I then want to travel to Istanbul - spending more time on Bulgaria after Istanbul rather than before. The journey from Istanbul to Plovdiv should be fine as in Istanbul for four days before the journey so can book that in advance.

Thank you for all our help, I am finding the Interrailing app and website really difficult to get any information on so this forum is invaluable!

Is there an international ticket office in all stations? I will be in Karlovo for three days, could I book Plovdiv to Istanbul from Karlovo station?

According to this list of ticket offices, Karlovo can only sell domestic tickets.