When you are outside of stealth detection range but within the Retribution range, the insignia will still appear above Skye even though she is invisible. Shoot below it for expected results.

Lead your shots. If you have a projectile, never shoot at her; even in close range you must shoot ahead of her. If you have a hitscan, wait until you have her in your crosshairs to shoot.

This may be Skye's worst matchup. With pluck, 1 shot and one empowered shot does 1820 damage. All you need to do is shoot her, hook her, and shoot her again. lel

You can Ghost Walk to cancel out his In Pursuit, or even better, his The Law. Save your Ghost walk for when he starts channeling his execute.