From a Reality POV: Many plot lines have been mixed around in the games and they may not go with eachother. It's just a game so sometimes you have to get over it.
From a "fan" POV: Well in AE the Glukkons didn't want him to come back all they said was (I believe this was Gen. Dripik) "If Mulluk ever comes back we're screwed!" Besides I can't see any reason for going back to Rupture Farms unless there's going to be something new to find in the "ruins".
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Abe-A-GoGo yotsu yubi wa warui
"It's All That Blue-Bastard's Fault!"
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