“Train of thought” means the subject or thing you are thinking about at a particular time. When you “lose your train of thought,” it means that you somehow got distracted from whatever you were thinking about. For example, when you are talking with a friend and trying to make some point, but then you forget what you were about to say, you can say “Sorry, I lost my train of thought.” Here, she is distracting him from whatever it was he was thinking about.

I agree with what John said. In the context of your story, the scent of her hair distracted him from what he was thinking. the phrase is usually used when you momentarily forget what you are thinking, or what you were saying because of something else. Hope this helps!