Most of us know that we're likely to loose our significant others when we transition.
It's one of the things that terrified me the most when it came to my own hormones.
I have a partner that's "pansexual" (basically it's like bi, except it includes androgynous and gender fluid people and so on just as easily) and loves me for who I am, not what's in my pants, and none the less, neither of us knew for a fact whether he'd still be as attracted to me once on the hormones, let alone once they hormones had worked their magic.
They will change your "boyfriend's" body and how it works to be more feminine, more "her".
Attraction to people is more complex than "men, women, or both". After all, you didn't fall in love with her (I'm sorry, I can't say him, it just doesn't work in my head) penis.
If she had some horrible accident and lost her whole set of genitals in 'em, would you stop loving her completely?
It's probably important to take it slow (without trying to make her wait longer than she can), for the both of you, and for you specifically to read as much as you can, even watch some documentaries, and try to understand what you can of what it is to be trasgender.
Communication is desperately needed as well, you guys have to sit down and talk about what you want from one another, and about children.
And you have to understand that even if you have children, it's probably for the best if she starts her transition while they're young, so that she'll be more happy/less stressed and thus have more to give her children as they grow up. You can't ask her to be an unhappy dad until they're all grown up.
It is always possible that you can't be with her after transition in that way, that the romantic and sexual aspect of the relationship dies down, if you are unable to overcome the changes to the packaging to still love the person she's always been on the inside. But you both should do your best to keep from assigning any blame to one another IF that happens.
You could come out the other end, the best of friends, with children that need you both to be happy and healthy to have the best chance of a good life.
You could also come out the other end a happy lesbian couple, raising children together.
You can't tell the future, and even if you could it would still not be set in stone 'till after the fact.
Talk, listen, read, learn, and try.
And try not to let the future spoil what you have today.
Love as much as you can.
And if ever it fails, remember her for the love, not for the contents of her pants.