In a "New Child" timeline, in which one assumes that OOT is a representation of the Imprisoning War/Seal War (that which inspired the AlttP) legend, as Nintendo once stated was the case, then a fully coherent line will likely have two seperate Ganons...

The IW Ganon will be the Ganon who is killed in tWW, the Ganon actually fought in AlttP wll either be a new character or the Ganon of Four Swords Adventure.

In any other case (where Ocarina Of Time is not considered to be the Seal War, as it the current popular oppinion... not that thatproovs it corret) then, for simplicities sake, they will almost certainly be the same Ganon.

(Edit: Concerning previous post, I'm considering one Ganon "Lifecycle"; A Ganon retruned from the dead (either resurected or reborn) may in facvt be the same man, but, in the consideration of my post, is essentially a "different" Ganon))