This will explain Emmy and Descole's disappearance for the main series. It's my way of explaining it, and it is not official whatsoever.
"I am not going to go so easily!" Over the sound of the screaming alarm and the countdown, Descole's desperate screams could be heard.
Professor Layton and Luke were barrelling across the room, trying to space themselves as far as they could from Descole's machine before it blew up. Emmy grabbed Descole's arm and tugged at it.
"Come on!" she shouted. "You need to get out of here!"
"No!" Descole shouted, lashing out. Emmy didn't see the movement coming and Descole's arm wrapped around her throat. She flailed and kicked, but Descole was too strong for her. "If I'm going to go down, a part of Layton is going down with me!"
"Please, Descole! You don't have to do this!" Emmy screamed, still kicking and flailing.
"Layton deserves to lose you! I want him to feel pain!" Descole roared. Luke spun round and gasped.
"Emmy!" he called. Layton spun round and made a beeline for Emmy.
"No, Professor! Leave this place! LEAVE!" Emmy screamed. "Go! GO!"
"I'm not leaving you behind, Emmy! As a gentleman-" Layton was cut off.
"SCREW BEING A GENTLEMAN, PROFESSOR!" Emmy howled. "GO! JUST GO! IT'S MY LAST WISH, AND YOU CAN'T IGNORE IT!" She was becoming extremely desperate, Descole still holding her too tightly for her to escape.
Layton stopped, bit his lip, then ran back to Luke. "Come, Luke. A gentleman cannot ignore a lady's last wish."
"No, Professor!" Luke squealed.
"5... 4..." the countdown continued.
"There's no chance of Emmy's rescue now," Layton growled and pulled Luke along as fast as he could.
"Goodbye," Emmy whispered, and the machine exploded.