ShapeShifting changed the spot.

[Syn]

But isn't suppressing memories more what the Haitian does? Matt Parkman literally controls brains, so I don't see why he wouldn't be able to completely remove a memory. After all, memories are just specific arrangements in the brain; the haitian made it so certain memories were severed but still there, but Parkman has the ability to manipulate the brain completely. Given that he was dealing with a super powerful psycho killer I don't think he would have done a half assed job.

[CompanyMan]

Since it took an act of healing to restore memories wiped out by the Haitian, it appears that the memory wipes by him are made by scarring the brain.

The Parkman whammy is different. Matt can implant telepathic illusions in another's head, but his power does not effect the brain itself like the Haitian's does. Matt himself was whammied in a simular way by his father and was able to "wake up" from it with out any need for healing.

So it appears that Sylar as Nathan still has his memories (as well as abilities) intact, but is under the impression that he is Nathan, at least until he somehow "wakes up" from the spell Matt put him under.