I think you're mistaking the Ability Capsule for a held item.
It's a one use item, and will disappear after it's used, meaning that the change is permanent, even if the Pokemon evolves. E.g. Ability Capsule is used on Marill with Thick Fat > changes to Huge Power > evolves into Azumarill with Huge Power.
It also only works on Pokemon with 2 possible abilities, like Marill. Hidden Abilities are not counted, and the capsule won't work on a Pokemon with 1 normal ability and a Hidden Ability.