I just took delivery of the Flex about 2 weeks ago. Everything looks and works well except the S Pen gives me quite a bit of trouble. About a week after I have start using my new laptop, there is an error message popping up as a message notification to the right side of the screen. It said "Connection error: Connection failed. Check the connection environment or the battery level of the S Pen". I have tried to reset the S Pen through the Samsung settings panel to no avail. I have called the tech support line and I believe he has re-installed the driver on my machine and it seems to work, but only for a few days because it came right back to where it was before. I called again and the tech guy won't able to help much. He did offer to send me a new S Pen and I'll see if that may cure the problem.
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I got the same error message and noticed that when it happens my bluetooth mouse disconnects. So the problem revolves around the bluetooth connection. It's not just related to the S pen. Is it the bluetooth driver or a hardware problem?
Try turning off bluetooth and turning it back on in your computer's settings, not samsung settings. It worked for me; pretty upstting such an expensive laptop has simple flaws.
I was able to solve the connection error and Air Action gestures issue by updating the bluetooth driver using the Samsung Update app. Now Samsung Settings shows the S Pen Air Actions are available with 100% battery. I verified that all of the Air Actions work. Good luck!
FYI, I had the same problem again this week. I reinstalled the bluetooth driver since that worked previously, and it is working properly once again. I'm not sure what caused the bluetooth driver to stop working twice within 3 weeks.
I had the same issue. I needed up having to go into the samsung settings under the s pen tab and click reset s pen. Once that was done and reconnected it started charging up my s pen right away. I haven't had any problems since. I hope that helps you too.