Trips that don't appear in the app you will have to enter manually.

You can add trains manually to the app. Scroll to the bottom at the train search and add the train to the app. 

But it does not make much sense to board this train (only running summertime-only 1 overnight, starts from Sofia) in D-gr, board at a major stop.

Also DO read seat61 and see that it will not bring you into ´proper´ IST but ends at some godforgotten suburban stop-from there, even though technically there are commutertrains by TCDD, you MUST first see to get a local chipcard and then put money= TRL, not €, on it and travel on. There are hardly -as for now- any trains left in TR-but definite reports about it are very sparse.

Thanks a lot for your answer @mcadv. I will take the overnight train, that arrives at 5:34 am at Halkali. From there it is 55 min by local train to the center. That goes every 15 min. Only I hope that I can add this journey to the Pass, since it is unfindable in the app.