Listen - that's all you can do. If you try to be proscriptive in any way, she will switch off and not confide in you.
Full disclosure - I'm a gender critical feminist, so though I fully support transgender people's right to get on with their lives as they see fit, I don't buy into the ideology that goes with it.
Having said that, there seems to be an accepted narrative in student/politically left circles that the right response to your male heterosexual partner deciding to transition is to say "that's wonderful darling, it is you as a person I love, let us move smoothly into a lesbian relationship while I salute you for your immense bravery." In fact, your daughter will be under tremendous peer pressure to buy into this narrative, even if she has some nagging suspicions that she isn't comfortable with the new turn in her relationship.
In practical terms her former boyfriend will be the same person - if he's been a nice guy so far, hopefully that will stay the same. (And chances are, from what I read of tumblr/student social lives these days, the actual transition won't go much further than donning a dress and insisting everyone "gets her pronouns right" - cf the Eddie Izzard thread in feminism. About 80% of transwomen retain their penises - a decision which I sympathise with as the surgery is complex and has a high rate of complications.)
So listen, let yourself be led by her, but watch out for hints that she is finding this hard. She may well need a space to vent some of her more negative feelings about it(she may well feel quite conflicted - part of her happy for him, part of her worried about what this means for her) future, and you may be the only safe person she can talk to, such is the pressure to be "on the right side of history" in student circles.
(There's a transwidows thread in feminism too - though that is largely older women whose husbands are transitioning for somewhat dubious motives, so may not be applicable to your daughter's situation).