On my Note 2, there's a setting to warn you if you walk away with the phone without putting the s-pen safely back in it's holder. Is there a similar setting/ warning on the GN10.1? I've looked everywhere but cannot see anything obvious.
Are you running Jelly Bean? Once I did the upgrade from ICS, I started seeing a new notification in the notification area "S Pen has been removed". After a brief moment, the message collapses to just an icon of the pen in the notification area. If you cick to expand your notifications, you'll see the message again in the "ongoing" area. Once you replace the pen, the message disappears. This appears to be a new JB feature. Opening up the Settings for the S Pen doesn't offer any options to turn that messaging on or off, that I can see? Under S Pen settings I have:
Pen attach/detach sound
Options after detaching Pen (determines which app to display, or whether or not to show the shortcuts toolbar)
Quick Command settings
S Pen Help
Same list of settings here (UK based); no warning setting either. Not sure where I find if I'm on Jelly Bean or not but in "about the device" it says I'm on v. 4.1.1 (the tablet was bought this week).
It would be a shame if they've dropped the s-pen alert on the 10.1. I do a lot of note taking and the pen is more often than not out of its holder so an alert if I go wandering off is really useful (or have I overlooked a setting hidden away somewhere in this OS version?)