Hi K.,
First, let me say, I think you handled the conversation with your boyfriend's daughter beautifully. You just focused on the truth, and stayed away from asking too much/putting too much focus on her mother's odd behavior. This was a lovely way to stay very safe with her.
This is a really hard one, but I do think that you should talk to him about this. The reason being, you do want to document this. Her mother having said something like this is important because it's a pretty huge red flag. You will have to help him see that, for his daughter's sake, he needs to keep his temper and talk to someone else ( a counselor, adviser, his lawyer if he has one,esp. if he's seeking legal advice in regard to parental rights and responsibilities) before confronting her. I haven't read your previous posts, but these aren't the actions of a well parent, to tell their child they might not truly be related to their father. That's just sick.
Your boyfriend can also, gently let his daughter know that, no matter what anyone says, he's always going to be her dad and she will always be his daughter. That they know, beyond a doubt, that they are meant to love each other, and this would be a great time for him to share with her some of those neat things they have in common: mutual loves and interests, and recounting some happy memories of spending time with her, and how he sees himself in her in positive ways. This will go farther than combating a vindictive ex. He should not mention his knowledge of what his ex is telling her, and let his daughter bring it up if she chooses to. He's just opening a door in the conversation, and reassuring her of his love and their bond.
Little kids actually catch onto which parent does/says/acts in ways that are healthy, consistent and respectful, and feel safe to be around, and which parents are harder to feel good to be with. Being told that your Dad isn't your Dad *doesn't* feel good. (I know this one personally!) This is why I suggest focusing more on keeping the relationship with his daughter a positive one for both you and your boyfriend, and giving as little attention to her mom, because believe me, it will come back to his daughter in a negative way that might make things more confusing for her. Keep documenting everything and best wishes.
H.