Can I keep my Apple Pencil 2 charging on my iPad Air all day?

Keeping your second generation Apple Pencil docked with your extended periods will not harm your Pencil - in fact, keeping the Pencil docked with its host iPad whenever it is not being actively used is recommended. Doing so will keep the Pencil optimally charged - and will protect its battery from damage.

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. You should 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.