I'm really sorry to hear she has that concern. (And also that I'm late to this: I took a few days off.) I certainly get why she does, especially if she knows or feels anything when it comes to the history of medical transitioning and how pervasive that attitude was -- the giant batch of bullshit ideas that fueled care being given only to people who conformed to cisgender people's ideas of what transness meant, and what was required for transition, including things like the necessity of dysphoria with genitals.
But trans care has changed so much, even just over the last ten years, and I'd be quite shocked to hear a current provider, with current education, not follow through with care they have otherwise okayed because someone was cool with their genitals and/or how they function as they are. If she is worried about things like this with her provider, I wonder if she's sure this is the right provider for her, someone she feels very comfortable with? If not, does she have options to switch to someone she'd feel more able to talk with honestly about things like this?
If not -- if she is comfortable with her current provider -- then I'd say she should go ahead and ask about this. But maybe before then she could have a conversation about having these kinds of concerns: worries about asking questions about the effects of her medical care and treatments (something every patient should be able to ask, with any kind of healthcare) because she's worried they'll disqualify her from medical transition. It seems to me that feeling confident she can ask literally any questions without having to worry that's an issue seems pretty vital to her quality of care and peace of mind, you know?