I'm not sure I follow what exactly you are saying. Aegis Boon blocks and restores HP based on how much damage you've taken, not based on how much damage you've blocked. Since your Stoneskin absorbed the damage and you took 0 damage, your recover 0 HP because you took no damage at all. The block activating during Stoneskin would reduce how much damage your Stoneskin itself takes so it could potentially be a free hit or more of Stoneskin, which is quite valuable.