In the second season finale, Jax's son Abel was kidnapped by Cameron Hayes (Jamie McShane).
Hunnam told TV Squad: "[Jax is] really not dealing with the whole [kidnap] thing very well. An interesting by-product of that is that it reunites [him with] Clay. That contention that had been building through the second season gets put on hold."
However, the actor insisted that old grudges could resurface in future episodes.
"[The past is] certainly not forgotten, because that's history that's never going to go away," he said. "I'm sure it'll resurface in a very violent fashion in the future."
He also revealed that the new season would instead see Jax clash with his mother Gemma (Katey Segal).
"I've got something going on... that's designed to protect her and the club, that she totally messes up and violates," explained Hunnam. "That creates a nice environment for Gemma and I to have a little bit of contention, which is a new dynamic between us."
Sons of Anarchy returns to FX on September 7.