Board Thread:Naruto: The Last Discussion/@comment-25824723-20141207101850/@comment-945885-20141215061259

They didn't regenerate. He pulled them back after throwing the Rasenshuriken (there's a panel where you can see them fly back). Truthseeker Orbs simply can't be generated or regenerated freely by the user. They appear when the user awakens the power of the Sage of Six Paths and are "always on" and can't be "created from nothing." If seperated from the user they can be "lost" (they can only be controlled within a range of about 70 meters), which is why part of their strategy against Madara was to seperate him from the Truthseeker Orbs.

Naruto started with nine Truthseeker Orbs. He used three to seal Madara's Limbo shadow. He lost one in Kaguya's lava dimension (the one Sasuke had been using as a platform), and two in Kaguya's original dimension (the ones he had stabbed into Black Zetsu after cutting off Kaguya's arm). He used the last three to trick Black Zetsu into destroying a Shadow Clone while sealing Kaguya. The next time he's seen after that he has Six Paths Sage Mode deactivated. When he activates it again to fight Sasuke, he only has three.

So Naruto either only has three Trusthseeker Orbs left (and lost six in Kaguya's dimensions) or he has six Trusthseeker Orbs, but never recovered the three that were used to seal Madara's limbo shadow.

To the best of my knowledge, there has yet to be an explanation of why he doesn't use Six Paths Sage Mode in the movie. We don't know if he lost the ability or simply chose not to use it. It might even have just been a matter of production, with Chakra Mode being chosen because Six Paths Sage Mode has yet to appear in the anime, or maybe even because they started production before Kishimoto had finalized details on the mode -- keep in mind that Naruto only used it for the first time in April of this year, six months ago.