Hi, thanks for asking!
This strange ‘Apple Pencil is possibly not connected’ message appears when you disallowed new Bluetooth devices to connect until tomorrow in the Control Center. It’s really weird, but technically in this very case we cannot determine if an Apple Pencil is connected, hence the conditional mode, while your Pencil might still be functional. To get rid of the red message, just allow it again in Control Center.
The Bluetooth connection button has now 3 states - which Apple introduced with iOS 11, and caused quite a bit of confusion, btw: http://www.idownloadblog.com/2017/11/14/ios-11-2-control-center-wi-fi-bluetooth-splash-screens/
Grey: Bluetooth is turned OFF in Settings
Blue: Bluetooth is turned ON in Settings
White: Bluetooth IS turned ON in Settings, but new devices were manually disallowed to connect until tomorrow in Control Center
What’s really misleading is, in this white state, although iOS displays the message: Disconnecting Bluetooth devices until tomorrow, in fact, they still allow Apple devices (Apple Watch, Apple Pencil) to stay connected.
And we know it’s weird, but in this white state, we technically cannot determine if your Pencil is connected…