If I have a confused or poisoned Genesect V with 2 Fusion Strike Energy attached, and my opponent has a Cradily with the "Swaying Strangle" Ability in play, would I be able to Retreat after I have discarded the 2 Fusion Strike Energy cards as the cost, or would I no longer be able to Retreat?
Since you began the Retreat process while Swaying Strangle was prevented by the Fusion Strike Energy, you get to complete the action and Retreat even after discarding the 2 Fusion Strike Energy cards. The behavior is also similar with Flygon's "Labyrinth of Sand" ability or Snorlax's "Block" ability.
BlockLabyrinth of SandSwaying StrangleFusion Strike EnergyRetreating