Hello, I have been playing for some time with two b wings and stocking them up with heavy laser cannon, adv. proton torpedoes, and ion cannon. I read yesterday in the paper core set rules that” a ship can perform an attack with a special weapon instead of its primary weapon”. Then today I looked at the online rules

Not normally. There are pilots and upgrades that allow for this. Stabilized S-Foils for the B-Wing or IG-88B allow for firing a cannon after a primary attack. IG-88B actually even lets you fire a cannon attack after a cannon attack.