A mother cat always starts out with a good relationship with her kittens - there's no question about whether or not they "get along," because that relationship is DEFINED by the fact that she's the mother.
BUT there comes a point when the mother instinct no longer defines that relationship, or even exists at all. Some relationships will continue to thrive while others will deteriorate, as they are no longer defined by instinct, but by the chemistry or lack thereof between the two cats.
Cats have a pretty good memory where relationships go, with people and other cats. It's hard to say whether or not she may "know that that's her kitten," because it's a moot point - even if she did know, she wouldn't care, so it wouldn't factor into her current relationship with her kitten.