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In Season 3 Episode 1, how did Sylar take Claire's powers?
Why wasn't she regenerating in the process?
Why did he have to place the top of her head back on her in order for her to heal, when she could just regrow it like she did with her pinky toe?
Why couldn't she feel pain if he didn't remove anything from her? He said "No nerve endings" why doesn't she have those?
And why did Sylar say "I couldn't kill you even if I wanted to."
Before they said she had a weak spot in her head...and besides could he just use his TK to cut it off and then explode it with his radiation powers?
Can she never die like he said?

The scene was really cool but very confusing lol. If anyone knows an answer to this please help!

He took them by studying how her brain works.
She probably would have regenerated a new scalp if Sylar had left her alone, but I imagine that would have taken longer than just replacing her existing scalp and letting it seal up, also the writers would have wanted to make it clear to the audience that Sylar wasn't just out to kill her.
And, I'm not too sure on the other questions, been a while since I've seen that episode.

It was always my understanding that Sylar "turned off" her ability to feel pain. She could feel pain all the way up until that point.

The weak spot wouldn't kill her though. Even if that spot was stabed into or shot her body would heal. She would just remain unconscious until the object was removed. Like what happened to Peter with that piece of glass in the head and Claire had that stick in the head. After it was pulled out they came back.

It is said in the series that someone like her (someone who can heal) will stop aging after their powers are activated. They would also heal from any wound. So her dieing is up in the air imo. If she was destroyed faster then she could heal and nothing was left of her then she could come back.

Didn't Claire tank a mini-nuke point blank in Company Man

iirc she took the equivalent. Ted lost control of his powers and started putting off a bunch of mini "bursts" but their was no full on explosion. I distinctly remember Bennett standing out on the Lawn right outside the house.

Yes