Voshavel: During WITH A LITTLE HELP FROM MY FRIENDS at the train tower, the romance option "[Stand by window] Missed you" does not appear. Up till now i did everything that was requested of me.
According to the guide book, the things that are required to romance her up to that point are to have a V with a male body, flirt with her at the end of Riders on the Storm, do not disclose Panam's plan to Saul at the begininng of "With a little help from my friends".
I replayed that mission to have the conversation again. I have a female V in my playthrough and that dialogue option does not appear even though I flirted with Panam during Riders on the Storm so it must be a male V option only, or possibly the website guide you are following was from a review copy version of the game and that dialogue got removed.
Either way, it doesn't matter if you choose that option during the dialogue, only that you do NOT choose the dialogue "Not doing it for free".