Flocke is not the smoke monster by timeisrelative

This theory explains why Flocke is not the smoke monster and why Flocke is already in the Temple.

Flocke may control the smoke monster, but they are not the same. Notice what happened in the scene where Bram and company assaulted Flocke. Flocke leapt behind a pillar. When Bram moved in, Flocke was gone. Then the smoke monster appeared in the doorway on the opposite side of the room. The mechanics of this scene do NOT suggest that Flocke morphed into the smoke monster. If so, Smokey would've been waiting behind that same pillar.

In fact, why would Flocke jump behind the pillar at all? Why not just morph into the smoke monster right away? Unless...he wanted people to think he was the smoke monster. Why? We don't know yet for sure. But strategically it makes sense. Flocke has the advantage of having an ally that no one knows about because they think he and the ally are the same being.

This leaves the question as to how Flocke disappeared into thin air behind that pillar. It would sound far-fetched without some kind of precedent. Fortunately, there's Harper. After Juliet was left to integrate with the Losties in season 4, Harper appeared to Juliet in the jungle to let her know that Faraday was headed to the Dharma station that contained the toxic gas. Harper's ability shows that the Others have access to this ability. (Or maybe just some faction of the Others. There's so many factions of Others these days.)

When Keamy and the freighter mercenaries arrived on the island, the Others moved out of the barracks to a place that is more secure. Ben told Alex to go to the Temple to avoid the mercenaries because it's the only safe place on the island. So it's reasonable to assume the Others living in the barracks moved to the Temple. Harper was living in the barracks which means she likely moved to the Temple.

Before Harper appeared to Juliet, her presence was preceded by whispers. Since we also heard whispering just before the Temple Others nabbed Jack and friends, the Temple may be the source of this disappearing/reappearing ability.

So for Flocke to be able to disappear and reappear, he would have to have access to the Temple. Perhaps his presence in the Temple is why the healing spring water was murky instead of clear. This water issue was quite troubling to the leader of the Temple Others, but he didn't know why.