It is what it is.
You cannot store Apple Pencils for any prolonged period of time and NOT keep them charged up to some level.
If your Apple Pencil/s sat around unused or unopened and not kept charged up for more than a few weeks, or so, OR
LONGER, then the battery in your Apple Pencil may have failed and is dead and you will have to purchase another
brand new Apple Pencil or get, if still under warranty, a free replacement Pencil from Apple.
Sorry.
And it looks like some things about the Apple Pencil have NOT changed in the new version 2 model, either.
FYI and something Apple will never, EVER divulge to it potential iPad Pro/Apple Pencil customers/users unless the potential customer/user is smart enough to ask about,
Due to the “always on and active/standby” nature of the Apple Pencil and, also, due to its very tiny rechargeable Li-
ion battery ( smaller than the eraser head on a REAL wooden pencil ), the Apple Pencil needs to be constantly charged up to some significant charge level ALL THE TIME, even when not using the Pencil for prolonged periods of time.
The Apple Pencil needs to be kept charged to a minimum of 5-10% all the time.
If the Apple Pencil battery is allowed to drain down to 0% and allowed to stay in that flat condition for more than a few weeks, or so, OR EVEN LONGER, that very tiny little Li-ion battery is too small to keep at a 0% state for a long period of time and it will fail and the Apple Pencil will be dead and you may have to “pop” for another $99 Apple Pencil, once again!
Apple only has a one-year warranty on any Apple accessory items.
You need to keep your Apple Pencil charged all the time, even if it is only to 10%-15% charge. It must keep some charge level in that tiny Lithium-ion battery at all times!
It is what it is.
Apple is quick to tout the latest and greatest, coolest features of its newly introduced mobile devices and computers, but like most computing product companies, no mention of any of its product weaknesses or pitfalls.
To this day, most average users do not know they need to backup the data on their mobile devices and computers to protect their important data AND most computer electronic companies do not post such information and procedures needed to do so, as it makes the computing products they design, make and sell, look susceptible and flawed, even though they actually are.
AND no computing device maker/company wants that!
Sorry, but this is the Apple Pencil's biggest flaw. That teeny, tiny battery.
It is too small to hold a charge for a prolonged period of time,
This is why I still use older iPad Pro models and another third party stylus option tbat still works with these older iPads tbat have a larger internal, rechargeable Lithium-ion battery and have a dedicated on/off button to better retain a full battery charge.
Again, this is a weakness of the Apple Pencil.
There is nothing to be done.
Sorry.