the bypass box was likely a data module for the remote start. I would have wanted to see ign, and only used that circuit as sense (not trigger). You tapping into the same ign lead should have done nothing to fry the bypass. It also does not "cut" any data wires/etc, so it being dead would not have interfered with the vehicle starting. It sounds as if you caused a circuit fault - perhaps blown a fuse - and without ign, the car will not start.