They actually find Judith already dead in the WN, with her head chopped off and smashed like a watermelon, which is apparently the only way to surely kill a vampire.
They spend another day together or something like that, planning to leave the dungeon because there's nothing for them here.
Just before they're able to finally leave, the Black Agetha shows up and chops off the other Agetha's hand. That's the reason I remember this is how this went. The conversation goes about the same as the manga, minus Judith ofc, then Black uses Reset.
There's not much change to the plot I suppose, but the interlude should have been one of the periods where Kiska gets to know Agetha better and come to care for her.