A couple questions...

Cohaagen says it: "the best double agent is a double agent who does not know he is a double agent" - or something to that effect. To really fool them he need to go deep undercover, and what better way than to do it completely. Also, since "brain poking around" is part of the plan, it is better to keep a clean slate, i'd say.

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** I am normally not a praying man, but if you are up there, please save me Superman **

I the directors cut it is revealed that Melina is Mathias' daughter, and that Hauser is sent into to seduce her and earn her trust, so he can get close to Mathias and assassinate him. The problem arises when Hauser falls for Melina answer switches sides. Cohaagen captures Hauser, changes his face and memories, and hides him with Lori knowing that the resistance will try to find him to get the code for the synth's killswitch.

His memory was erased to 1)keep him docile as Hauser presented a real threat to Cohaagen and his operation, and 2) so he would function as a plant to draw Mathias out. I hope this helps :)