Not likely, since the Phantom Bullet arc occurs before the Caliber arc. (Sinon was present during their quest to get Excaliber, after all, and was integral to the events there, so it wouldn't make sense to appear before the story in GGO.)
I'd say there are basically three possibilities here:
1. They completely skip the Jotunheim and Caliber stories. (In which case SAO fans in both Japan and other countries are going to pissed all around.

)
2. They do Jotunheim+Caliber in two or three OVA episodes.
3. In season 2 (if there is one) after the Phantom Bullet arc, they do a flashback episode to Kirito and Leafa's adventure in Jotunheim and then do the Caliber story in the following episode.
Personally, I'm betting on number 3, since I don't think the Phantom Bullet and Mother Rosario arcs have enough material for a two-cour season by themselves, and stretching out the material for them would just make me pissed that they didn't so for the first season as well. But, in any case, first we need to wait for the official confirmation of another season anyway...