If a card is shuffled into a deck, is it also (by definition) negated? I don't think so, based on Captured Ark:
Captured Ark (P)
Type: Curse • Brigade: Crimson • Ability: 1 / 5 • Class: None • Special Ability: Upon activation, each opponent must select one active Artifact in own territory and shuffle it back into their draw pile. Each shuffled Artifact is negated. May be used twice. • Play As: Upon activation, each opponent must select one active Artifact in own territory and shuffle [return] it back into their deck. Negate each shuffled Artifact. May be used twice
