Kyle did kill Boba Fett. Fett didn't die at the Pit of Carkoon. The pit spit him out because of his manlorian armor. You killed Fett in Dark Forces.
Dude, Dark Forces takes place before RotJ. Plus, Boba isn't killed, he flys away when you prove to be too much for him.
Same applies to MGS2. I haven't actually played the game, but I understand it was suppose to have happened before MGS1.
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