Had the same problem.
I just re and disconnected a few times and then it worked.
However I can't guarantee it'll work.
I know how to solve this, as I had similar issue. I hope an admin can add this to the FAQ guide of Ninebot Flasher.
Here are the steps:
1. make sure your smartphone's bluetooth is off, so it cannot connect automatically with the scooter
2. turn on the scooter, you will normally see the bluetooth light flashing - This means it's searching to connect
3. open the ninebot flasher in windows (make sure your computer's bluetooth is on)*
4. press Start Scan
5. IMPORTANT: once you have found your scooter, press Stop Scan => I didn't do this step before, and I almost always failed to connect.
6. press Connect
*if you don't have windows but mac, you can install Bootcamp from the official apple website, so you can install windows home 10 for free on your mac, next to your existing MacOS. This works. I do it like this.