As I’ve said, since it doesn't say the money came from Emma's mother, or someone else, I think it's money she will inherit from Mr Woodhouse. However, even if part of it from her mother, Mr W might have a life interest. Regency society was patriarchal, it was very unlikely that unmarried daughters would have complete control over their own fortunes in their father's lifetimes, while married woman would have their fortunes under their husband's control (unless her marriage settlement specified that she could have control). I think it's quite certain that she will have the money, so it's spoken of generally as hers. Perhaps there's a settlement e.g. in P&P, when they got Lydia married to Wickham, there was a settlement that she would get an equal share of the 5,000 pounds after the decease of Mr and Mrs Benent. So perhaps, when Isabella married, there was a settlement that each daughter will get an equal share of teh funds Mr W would have to leave -- and it happened to be 60,000, so it would be 30,000 each. Also, in Emma's case, her invalidish father was not an authority figure, so even if the money was legally his, it could be she who actually managed it.