SOLUTION? Go to 2nd paragraph for solution. The first one is how I thought I broke it.
I had the same problem. I used it in the shower, I got shampoo on it so that I wouldn't get shampoo or water on my phone screen. I rinsed it off and when I got out of the shower it started randomly pausing and playing my YouTube video when it was in my in my phone. I thought I had water damaged it or something, so I did the obvious (obvious to a tech enthusiast). I used rubbing alcohol to hope to vaporize any water left in the pen. What I failed to do was turn it off because there is no off button for the s pen. After doing that I realized my mistake and realized I could have just ran the capacitor (battery) down by pressing the button 200 times. After I did the rubbing alcohol it would not connect to my phone wirelessly. It still worked as if the "S pen remote" option was off. I did try restarting the phone with the s pen out of the phone, but it didn't work.
I switched my mom's pen with my own and both worked fine. So I switched them back and they both worked fine. I know not everyone has another Note 9 available but for now stores will have them on display, so you could try that or ask their desk person of you can try that. I'm thinking of Best Buy because they have the display and the geek squad/ nerd herd (Yes a Chuck reference it is a great show).
Mine won't connect and from what I read, the issues is with the S pen. So can I just have the Sprint store order me a new one for free because if they think I'm using my insurance to pay $200 for a faulty pen, they're nuts.
Have you already tried resetting the Spen?