Tom,
You’re on the right track. You do not have a free hand with things that the players paid for. If they paid for it, you’ve got to attack it with builders or conflict scenes. And you should! Everything on their character sheets is in jeopardy. You can’t just whisk it away, but you can fight them for it – you can make their possessions and relationships even more meaningful by thrusting them into the conflict.
In my BE game on Sunday, I got into a DoW with the PC Psychologist FoN. My statement of purpose was that he was to execute his staff, including his beloved relationship with his smoking hot grad student. The player balked, “No way! Uh uh, I can’t accept those stakes!” And I was like, “What? Are you kidding me? What the hell did you write that relationship on your character sheet for if not to put it in jeopardy?” He agreed, and we went to war! (I lost, btw).
Also, you certainly don’t need a phase intent just to ice a PC. You can kill one in a freaking building scene if you can corner him and stab him in the face. That’ll put the fear of god into them!
Re building scenes: You get three tests in a building scene, so you can absolutely circles someone up (1), subdue them in Close Combat (2), Hull them with Surgery (3). Badabing, new Vaylen in one building scene.
Re Infection mechanics: You do not get to say “Yes, but not really!” If the players win an Infection roll, they get to describe the results in a sequel. That’s hugely powerful – they get to establish a host of new facts about the world!
-Luke