While setting up the characters during development of the prologue, Daphne probably went through the most iterations out of all the characters. I always wanted her to be a headstrong character who's not afraid to speak her mind. In some way, she thus often serves as a catalyst for the other characters to state their own opinions, which makes her an absolute joy to write.
However, and I think you gathered as much from the early parts of the prologue, she also has a serious and vulnerable side. Her past will be dealt with during Trachi in some degree, but I'm planning to save most of it for the inevitable sequel.
As for Trachi, her role within the group is two-fold. Her main objective is to facilitate and maintain a channel of communications between Ionia and assets within the Trachian administration. So in some way, she's a liason.
The second, more unofficial part, is for her to ensure that Atlas will fulfil his objective according to the mission parameters. But, and I think you gathered as much from the prologue already, her interest in him is not exclusively professional.
Beyond that, however, a big focus will be in her interactions with Ganymede, as well. The two of them will come to work together in several instances and we'll see her trying to come to terms with her role as a guide for him, while Atlas is out doing Atlas things. In the end, I think the relationship between Ganymede and Daphne will be one of the most interesting threads to follow not only within Trachi, but beyond.