I personally think you've done the right thing so far. For all you know, the father was happy with just seeing her one time and he'll go back to his life as usual.
There is a lot riding on whether or not he's serious about making a commitment to her. I would be leary that it's taken 5-1/2 years. But, that's not to say that he isn't sincere. He may be more sincere than ever now that he's met her.
I would swear your older kids to secrecy for now and contact a therapist who specializes in children....children of divorce and blended families, etc.
I think that you, the dad, and the father should meet with this person prior to saying anything.
Whether father stays in her life or not, she will need to know the truth but there are ways you can approach it in terms a child can understand.
Little kids perceive the world differently than adults do and sometimes keeping things simple is best. But, you need to be prepared for whatever questions she may have.
My daughter had a wonderful therapist (for a different reason) and she always said, "Don't give too much adult information".
I would start with seeing if father is willing to talk to someone about how to explain things. If he's not, that would be a red flag for me.
You should be able to express your concerns and he should be willing to listen to how disappearing again would affect your daughter. Not just you saying it, a professional.
That would be my advice.
Then the therapist could lead you in a certain direction and suggest books, etc.
I would have some kind of game plan before disclosing all of this, but that's just my opinion.
Best wishes.