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Since Storm shields now add +1 to the dice roll, does that mean that the AP is now -1 and therefore ignored by Salamanders?

No, because both the storm shield and AP itself affect the dice roll directly. Plus the storm shield buff is its own effect, and isn't directly related to AP.
Or to put it another way - you roll the die, add the 1 and subtract the 2.

Miradorm wrote:
Since Storm shields now add +1 to the dice roll, does that mean that the AP is now -1 and therefore ignored by Salamanders?

No, because +1 to saves is not the same as reducing the AP of the attack by 1. An AP -2 attack against a 3+ save model with a Storm Shield is still AP -2, you just roll D6+1-2 for the save. The modifiers don't cancel each other out, they simply apply cumulatively.

Thank you both. I kinda had the idea that was what it was, but just wanted another opinion just in case.