My Apple Pencil is working just fine, but the alert dialog doesn’t go away. (In case you didn’t know this was happening).
SOLVED: Something happened that I needed to re-connect my Apple Pencil with my iPad, (forgot device, re-add device)… May have nothing to do with Shapr3D… 
One of my biggest issues with ePencil and my iPad Pro is that the iPad Pro seemingly “forgets” that the ePencil exists for some unknown reason; I have discussed this with support but I don’t think the problem has much importance attached at this time because you can simply reconnect the ePencil to the iPad via the port and it works again.
I have been unable to determine any situation as I kill all background processes when I work with the ePencil. I have had this same problem with other drawing applications however I have never seen an actual alert; the ePencil just stops works. Please note that I do keep the iOS updated.
Just wanted to add my 2 cents of information.
Hi, thanks for asking! 
In short:
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.
In detail:
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/
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…
Peter