Yes she is, see Uncanny X-Men #431
Maybe Aoa Magneto wasn't aware of the fact, or maybe he just didn't care.

@Blood1991 said:

Lol its complicated, from my understanding she was orginally brainwashed by Magneto to think she was his daughter, then it was proven that she wasn't later on and then I think House of M made her his daughter or something. I dunno it's just a colorful little plot device waiting to happen.

But in x-men legacy recently everyone referred to her as magneto's daughter even polaris called him father

She is confirmed as his daughter but this was only discovered much later in both their lives so AoA MAGNETO probably never knew about her and as such had no reason to care what happened to her...

@xerox_kitty:

There were writers back in the early 90s that wanted to turn her former relationship with Magneto into a pivitol and volitile issue. From 1993 below.

But, any plans the writer had in X-Factor for it never made it to print. Then in 1998 in Mutant X we had 616 Havok fall into an AU universe next to ours where Lorna is Magneto's daughter. It was a 32 issue series and it set up what a Lorna and Magneto father/daughter relationship might look like. It also was a big part of the reason I suspect writers decided to bring Lorna to Genosha and start rebuilding or since it was retconned to be a robot, building their 616 relationship there in 1999-2000.

Then in 2002 Morrison decided for whatever reason to have Lorna call Magneto her dad on Genosha and Austen followed up on it by filling in the blanks before the story with the DnA test and the rest.

I suspect next month in X-Men Legacy we will get the offical 616 history of Lorna's mother from Magneto. Years ago we were given the House of M history of her.

@xerox_kitty:

Well, she was repeately calling him her dad in Morrison's issue with her on Genosha even after her memories of the dead had left her mind and it was clear she knew what was going on and what Magneto had done with the memories of the Genoshan people. And, a few months earlier Austen picked Havok up from Mutant X where they were playing up Lorna's parentage big time in the final issue. Given he read Morrison's New X-Men 132 and the last issue of Mutant X below which Havok was in before he brought him to Uncanny he simply believed Marvel was going back to the plotline again (which at the time given the comics he was reading at the time with Polaris in them both 616 and Mutant X it wasn't a far fetched notion) and editoral didn't tell him differently so he furthered it during his run.

Though without Bendis and company furthering the story in House of M which was a massively popular storyline and lead to her being in WATXM the storyline might or might not have been retconned again we will never know. I happen to think Carey would have still furthered her parentage storyline when he picked her up from space, but it would be alot less popular with fans today.

As for Austen's depiction of Polaris, I actually thought he got power mad Lorna down quite well if one goes by a Claremontian view of it. Remember her powers were stuck on high non-stop on Genosha for many days if not weeks. It damaged her nervous system in a similar way to Magneto's nervous system gets damaged if he overuses his power. And, how does Magneto act when his nervous system gets damaged.... extreme mania with a large dose of megalomania which was pretty much how Lorna acted in 2003 and to a lesser extent 2004.

Think about Magneto's behavior when his nervous system is damaged and he is going on a power based insanity bender and then compare it to Lorna during the Austen era. Its like both of them are on methamphetamines and feel they can do anything and act however they want because they were superior to everyone else. And, its especially bad when they are powered up, they can at times pass for normal when they aren't powered up when they have a damaged nervous system, but they aren't.

Notice how once Xavier gets her to power down its like a 180 degree change in the character. Austen was very much following Claremont's view on why those using electromagnetism at too high a level become mentally unstable.

@xerox_kitty:

Here is Austen responding to fan questions about his run years later.

Since I hear a lot of these questions over and over again, I thougt I’d just answer a few and be done with them. These things never get covered in interviews, so it seemed a good place to get this stuff out there because for some reason people want to know.

So here we go.

Justin asks: I really liked your work on Uncanny X-Men, especially with what you did with Polaris. You turned her from a character that was always in the background who I hardly ever noticed into one of my favorite characters and you managed to give her character a nice edge. One thing I was wondering is how the decision to make Polaris Magneto’s daughter again came down? Was that Morrison or your idea? Because, I know the storyline had its roots in Morrison’s New X-Men 132 back in September 2002.

I believe it was Grant’s. But the roots went much further back, though others can tell you specifically when and where, what issues, what the circumstances were, which page, what panels, what characters, the costumes they were wearing, who lettered it, and possibly even the type of printer it was printed on.

There was a storyline done years ago where she was ‘revealed’ to be Magneto’s daughter, but then it was undone, or proven not to be true, or only happened in one of Scarlet Witch’s continuity-scrubbing bubbles, or something. Maybe in the Neal Adams Roy Thomas run. I researched it at the time, but I’ve since forgotten. I needed to memorize someone’s phone number, and that’s the only brain space I had available.

Apparently Grant made a decision to go back to it, but I’m not sure whose actual idea it was: his, Marvel’s, or God’s acting through them both as a conduit—I assume his, because he was Grant Morrison, and he had the power, the power of Hoodoo—all I can tell you is that the germ of the idea wasn’t mine.

I had intended to use Polaris in my run from the beginning, keep her much as she’d been when I’d read about her in X-Factor and other places, then eventually marry her off to Alex, happily ever after—at least until some other writer came along and made them related to Satan. It was a surprise to me when she appeared in Grant’s X-Men—crazy, muttering to herself, and wandering in the radioactive mud. We’d just had coffee the previous day, and she seemed fine. Just shows how you can miss the little signs.

Once she’d appeared as Nutso Profundo I had to rewrite some of my scripts, and went with Lorna the edgier, more volatile and unpredictable Looney Tunes with a heart of gold. It made a certain amount of sense, and I agree with you, she became more interesting than she had been. CURSE YOU GRANT MORRISON AND YOUR GENIUS! He was always making me look bad for my lack of imagination. I think he did it on purpose.

If Lorna had been on Genosha when it was destroyed, that kind of devastation likley would have changed her, deeply, although I’m sure she still could have had kids, a marriage, and sold Tupperware in her spare time if only I had let her. I decided not to, because I’m a dick, that way.

So it wasn’t planned, it wasn’t actually my idea, but I ran with it and thought it was a good direction and an interesting one. And, tellingly, people both credit, and blame me for the change.

If you liked it, I did it. If not, it’s Grant’s fault.

See how easy that is?

http://forums.comicbookresources.com/showthread.php?t=195337

He thought and still thinks what he did with her was great, Polaris fans are divided on the issue online. Most weren't happy with the love triangle and didn't like how he depicted her to start with, but at the same time most also do like what he did with her in late 2003 and 2004.

Also, he isn't blaming Morrison he is simply stating the reality that after New X-Men 132 in 2002 where you litterly had Lorna for weeks in the ruins of Genosha recalling in her head the last memories of the people who died there (which takes the cake for horrors the character has been through by far) he felt he had to go back and rewrite his scripts for Lorna. Austen's origional plan was to bring her back, have her marry Havok and then dump her and Alex into limbo, but New X-Men 132 altered his course for the character.