How does the Injured Pilot Crit card affect the IG-2000 title? Does it negate all pilot abilities gained by the title? Does it negate the pilot ability for allies gaining it through the title?

From the FAQ, under IG-2000:

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An Aggressor equipped with IG-2000 that receives the Injured Pilot Damage card can still use the pilot abilities of friendly ships equipped with IG-2000, but those friendly ships can no longer use its pilot ability.