Huh what? Im in confusion Σ( ￣□￣||)

Basically the system still had J registered and never removed when he was deemed "dead". But once he returned from the Rift the system recognized J's return and so brought him back into the Hunter ranking.

But why did the system not recognize him before?

Nonono. The system knew J, that's how it's able to track his activities to the point that it ranked him number 1. It just so happened to do so when the ranking got announced that year