Preparing an Apple Pencil for storage (Hibernation)
Setting aside an Apple Pencil for an extended period, without properly preparing it, risks failure of its battery. If deeply discharged, the battery may not recover from deep discharge.
While Apple has not published the process to fully shut-down an Apple Pencil, it is possible to do so by carefully following some simple steps.
An Apple Pencil prior to initial device pairing will be in its shipping state - where all of its electronics are effectively shut-off. In this state, the Pencil's battery is using no power at all - and can survive without charging for many months.
After the device is paired with its host iPad, when motionless the Pencil will automatically enter its low-power "sleep" state - where the Bluetooth radio is shut-off to save power. In this state the Pencil's accelerometer remains active - and will fully reawaken the Pencil with the slightest disturbance or moment. When sleeping, the Pencil's electronics are still semi-active - and will slowly deplete the Pencil's tiny battery.
To place an Apple Pencil back into its hibernation/shipping state, you must follow a very specific sequence of steps:
1) On the host iPad, ensure that the Pencil is fully charged
Settings > Apple Pencil
2) On the host iPad, open your Bluetooth settings; the Pencil status should show the Pencil as Connected
Settings > Bluetooth
3) On the host iPad, temporarily fully turn-off bluetooth
Settings > Bluetooth - set to OFF
4) Set aside the Pencil somewhere that it will not be disturbed. Any movement will re-awaken the Pencil - and prevent the Pencil from fully shutting down. Leave the Pencil undisturbed and totally motionless for at least an hour.
5) You can re-enable Bluetooth on the iPad; verify that the Pencil show its status as Not Connected. Should you choose to do so, you can remove the Pencil from the list of paired Bluetooth devices; simply tap the corresponding blue “i” icon, then tap Forget This Device.
Provided that the Pencil remains undisturbed as directed, it will fall into its low-power shipping state; you should note that there is no external indication that the Pencil is hibernating. A healthy Pencil will retain its charge in this state for several months. Being fully charged prior to hibernation will protect the Pencil's battery from damage through deep discharge.
Pairing the Pencil with an iPad will recover the Pencil from hibernation.