
Well, Reki Kawahara took to twitter and gave some context to the fans.

So why did the anime production team decide to adapt volumes 4 for the second movie? All of which are crucial for the story in the Scherzo of Deep Night. After all, the two arcs in volumes 2 and 3 contain numerous important story elements, such as new characters, events, places, and many others. This decision clearly sparked some questions among the fans.

If the first volume told the story of their adventure conquering the first floor of Aincrad, the fourth volume will focus on the fifth floor.

The upcoming second movie, however, skipped volumes 2 and 3, and goes straight to volumes 4, Scherzo of Deep Night. The first SAO Progressive movie adapted the first volume of the light novel, Aria of Starless Night.
