I watched the entire Hunter x Hunter series and I've just noticed that it is not stated whether Gon got his Nen back after being healed by Nanika or not. And I'm curios... once he jumped so high on the Wolrd Tree (we also have to notice the speed) is it possible that his Nen was restored? It would be impossible for a person with the qualities of an avarage human to jump so high/be so fast after all...
From wikia :
According to Killua, the degree of wish that Nanika can grant is probably infinite
Killua ask her to "turn gon back to normal" so Nanika saved Gon turn him back to a "normal" kid, he nen is closed now. Ging say this to Gon in the chapter 345 he had returned to normal.
I believe that Gon's aura is still there just not nearly as much as before. i think he gets it back or something because after Gon meets his dad and he and Killua split ways, Gon and his father fight together in the Dark Continent Arch. I'm not sure what happens in that arch yet because I haven't read the manga just yet.