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i guess the cold ice caused him to rejenerate more slowly or maybe he was just living underwater until he recongnised his friend's (attempt at) rechargation.
the Deoxys that was an actual Deoxys and not one of those double team things that picked up people, was Torri's friend yes. The rock the scientists were trying to rejenerate (they succeed near the end) was the second. The light think was the only part that Deoxys himself was able to rejenerate.
They're simply were always two deoxys, one was just still in stone form.
There are two Deoxys': one that emits out a purple beam and fought Rayquaza from the start. The second one is emits a green beam and appeared near the end of the move.
The first Deoxys regenerated much later because it took a hyperbeam point-blank and was reduced to only it's core. Regenerating a whole body takes much more time than regenerating an arm.
The second Deoxys, for some unknown reason, was low on energy and therefor couldn't change to it's humanoid form. I think it's low on energy because after the Tory and the other exposed it to some energy lasers that Deoxys regained it's humanoid form.