The journey would count as 2 pass days since the departure day is what matters.
2 options to use a single pass day are now possible :
- regular ticket for the night train (57€ per person)
- regular ticket for Berlin - Prague : 602 CZK (25€)
Since I've told you on the other post that the night train would be cheaper without passes I'd choose that option. Book in advance since it's a popular route.
From March the night train will go directly from Brussels/Amsterdam to Prague, it will be quite helpful ! :)
Don't expect to make the 07:04 connection out of Berlin. Maybe you'll be able to but not sure. Since reservations are optional (recommended on weekends though) you've got flexibility with the pass. You make the train ? Good. Otherwise have breakfast around Berlin main station ;)