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If I take sternguards and upgrade them with stormbolters, would the special issue ammo still apply? Would they become assault 2 special ammo?
No, it would not. The special ammo only applies to boltguns and combi-weapons.
Besides which the special ammo replaces the weapon's profile, this also includes Type. A stormbolter is Type: Assault 2, while all the special ammo is Type: Rapid Fire meaning if it were allowed then the stormbolter would be Rapid Fire for the special ammo shots.