It is generally recommended that a second generation Apple Pencil, or Apple Pencil Pro, should be kept docked with the host iPad when not in use - as this ensures that the tiny internal battery is kept optimally charged when not in use. Charging only occur when the battery requires charge from the iPad, optimal charge being entirely automatic.
Keeping the Pencil separated from the iPad when unused risks allowing its battery to discharge; if allowed to remain in this state, the battery may fall into a state of deep discharge, this being a state from which it may never recover. When the Pencil battery fails, the only remedy is to replace the entire Pencil; the battery itself is not a serviceable item.
Charge your Apple Pencil and check the battery - Apple Support
In more detail, all rechargeable batteries, regardless of battery chemistry, require maintenance through periodic charging. In this regard, the battery within the Apple Pencil is no different to any other device that is powered by an internal battery.
If your Pencil has been set-aside for an extended period, unused and uncharged, the Pencil battery may have been irretrievably damaged through deep discharge. In common with all Li-ion batteries, they must always have some level of charge.
The tiny internal Li-ion battery is susceptible to permanent/irreversible damage through being left discharged for long periods. Even some “new” pencils can exhibit signs of failure out-of-the-box if they are “old stock”.
It is essential that if you have an Apple Pencil that you charge it regularly - whether used or not - so as to protect the battery from deep-discharge. Do not allow a pencil to remain in low-charge state for any period of time - as the internal battery will fail, rendering the Pencil useless. Setting aside an unused Pencil, for extended periods, is a recipe for premature death of the Pencil battery.
If the Pencil Battery has failed, the only remedy is to replace the Pencil. If the battery has failed and your pencil is within its one-year warranty, you should look to having it replaced by your retailer or at an Apple Store.
Some reports suggest that gentle warming of the Pencil (such as a hot water radiator) prior to attempting charging of the Pencil can resurrect a Pencil battery.
