If you change trains after midnight, you need a new travel day. The scheduled departure time is all that counts: on a travel day, you can board as many trains as you like. The arrival time is not important and can be after midnight.

But no direct trains are there from Amsterdam to Prague. So it’s not advisable to take any night trains because it will always count 2 day pass since there are no direct routes.

Well, if you have a flexi pass, then yes… but on other hand you will save on accommodation which is pretty expensive this year.. Also keep in mind this point.

That is only true if you change after midnight. You did not give details about your schedule.

I am talking about the itinerary I attached now and highlighted the “change” train, because technically it is still supposed to be the same trip but I have to change trains in between to get to the final destination which is Prague. 

That's indeed a journey with a change after midnight, which will cost 2 travel days.

You could theoretically also travel to Zurich during the day and then take the night train to Prague there. That would only cost one travel day, but it would take so long you'd be better off just traveling to Prague directly during the day.

You change trains in Regensburg, arrival 5:05 departure 6:15. So that's a new day.

Yes I figured that much. Thank you for the clarification. It helps a lot in making decisions and changing the itinerary now. 

Take the overnight from AMS-and DO note many trips are fully booked now for summer hi-season- as far as you can-closest by to Paris and see what a normal ticket to P would cost from there on cd.cz.

OR go all the way to Wien (Vienna maybe for you)=arr mid morning-arr on NJ is always late at least 1 hr-and then use the cheaper RegioJet yellow train do Prahy (I often paid just 10€ for 1st cl-but as senior)
cheapest replace for passday is most likely: SEAT only-from AMS to Dusseldorf or KÖln, change to overnight ICE 618 to München-arr 6.00 next morning, then use BUS do Prahy from close by BUSterminal (also RegioJet and some others).

Thank you very much! This really sounds complicated and really doesn’t maximize the use of my global pass and not to mention taking into account dragging luggage from one transpo to another let alone more than one changes of transportation. It’s too much work and I’m not 22 anymore.