Emma can be Fraulein.
This is my current theory as well. After the meeting in Newport Emma kept tabs on Zoe. And when Zoe was suddenly in two places at once at the hospital, Emma intervened to buy the doctors' silence and move her comatose body to a secure facility. Helena Chang may in fact be the one observing Zoe, but as Emma's employee. As far as Gabriel, Reza and Wati know, Zoe has woken up with major memory holes. When Zoe took off for Europolis with Reza, Falk Friedman and Dr. Zelenka were hired to keep tabs and try to prod her memories to the surface. Wati was content to use Reza to monitor the state of her memories until Zoe started using a Dreamachine. They couldn't access her mind with it but I think Zoe started putting out signals uncomfortably similar to Faith's effect on Dreamnet; that's why the Eye showed up to capture or kill her.