If you add the train manually to the app, then only 1 travel day should be used.

For anyone else who ends up taking this train, I contacted cd.cz customer support and they said I should be good to use the rail pass and just needed to book a reservation. So as noted above, I added the train manually, booked the reservation, and I’ll report back afterwards if I had any issues.

@Camilo. Can you please look into this? The Railplanner should not use 2 travel days for a journey where the traveller doesn't change trains.

I will report this, but I cannot promise the changes will be visible any time soon. For now, it is a good advice to add the journey manually. 

Have a lovely week!

UPDATE:

Apparently DB shows Bohumin as a stop. For now, please book a seat at CDZ or at the train station, and create the trip according to the details printed on the ticket - however, there may be interruptions in the journey and the customer will have to use replacement transport (such as buses) to complete the journey.

Meanwhile, an investigation is being conducted.

I noticed the same problem thing when added the trip in the app for our trip Krakow-Budapest (nighttrain) last week. Same “change” in Bohumin. For us it wasn’t a real issue because we have an 2months continues pass. But I was wondering how this would work when you have a pass with a limited travel days and could solve it. 

 Indeed no factual change - the wagons and locs are doing an exchange of routes and coupling / decoupling but you can stay in your (booked) bed. 

You can then add the train manually as a direct train.