When a change in the distance between the outer shell and the proof mass is detected, it means that the outer shell has been influenced by non-gravitational forces and moved relative to the proof mass.
The outer shell thus protects the proof mass from nearly all interactions with the outside that can cause acceleration, except those mediated by gravity, and by following the proof mass, the outer shell (which is to say, the rest of the spacecraft, carrying instruments, etc.)
[1] One way to think about a zero-drag satellite is to see the shell/proof mass setup as being an accelerometer, measuring the acceleration of the outer shell.
Two such missions were NASA and Stanford University's Gravity Probe B (2004–2005)[2] created to measure spacetime curvature near the Earth, and the ESA's GOCE spacecraft (2009–2013)[3] which measured variations in the Earth's gravitational field.
Planned zero-drag satellites include the STEP experiment, and the LISA and DECIGO gravitational wave observatories.