Achilles' Heel was written with damage immunity in mind, though mainly immunity to the original source of the damage, and us wanting to avoid the extra damage being affected by that as well. Fortunately this is an easy fix, in that you can simply go with damage from Achilles' Heel always applying, no matter what Reduction or Resistances the target may have.
For the record, we're generally opposed to Damage Immunity (lethal), not just because of situations like this but because it hedges into undesirable territory (similar to the heinous "you may only kill this beast with magic items" issue with the mothership game). Sometimes what makes perfect sense in the narrative leads to less than playable rules, and it's best to either tweak your story to support more playable mechanics, or to accept certain compromises in the system to avoid potential conflicts.
Hope that helps!