Situation is Vessery is shooting someone with proton rockets. Tractor beam hits, does that ship loose -1 attack die if he fires his rockets after being hit.

He loses 1 point of his agility value per token, which in turn may reduce the number of dice he can add to a Proton Rocket attack.

Agility is a fluid number just like PS is while in the game.

That Tractor beam will temporarily lower the ship's agility just like having a Stealth Device still equipped would increase the ship's agility and potentially damage output with a Proton Rocket. The base number may still be there but the Procket just looks at what the Agility is NOW.