Atom interferometry based sensors provide today the most precise measurements of time, inertial forces and magnetic fields. In the common approach, a superposition state is interrogated for a given time interval and finally destructively measured. Conversely, we can repeatedly probe non-destructively the same quantum system and demonstrate efficient measurement schemes using feedback. First, we protect a spin polarized atomic ensemble from the decoherence induced by a synthetic noise. After the noise action, the state of the atomic system is read out with negligible projection using a non-destructive probe, and later corrected with a coherent manipulation to restore the initial state. The efficiency of the feedback scheme is studied versus the strength of the measurement and a maximum is found from the trade-off between information gain and probe destructivity. Our feedback controller is then applied to stabilize a classical local oscillator on a collective quantum state, and this is used in an atomic clock configuration to demonstrate experimentally that in some contexts a hybrid phase and frequency lock can surpass conventional atomic clocks which rely only on a frequency lock