Ok, so had a bit of time to tinker, and I can confirm that Joycons are working perfectly in 4.7.19. Seems it's a bug in 4.8.

Now - any tips on getting them to sync at startup - I find I have to be very precise to the moment I turn them on during boot up, otherwise they don't pair!

@Teeqla I was skimming the internet trying to do a project similar to yours and was wondering if you have had any success with the Linux Joystick Mapper and if you might be able to share it if you have?

I also tried xboxdrv recommended by someone on reddit, that didnt work too

I've got the first twist on Nickell Andrew (riking) running.
When I start the Joy Con driver via an SSL-Shel it works fine.
But I do not manage to start the driver automatically at system startup.

@Jean I have used the Linux Joystick Mapper program in the past to map the mouse to an analog stick for use in DOS games. I have no experience with using it with the Joy Con controller so I don't know if it will even work. You may wish to check this video first before you proceed.

If you wish to use Linux Joystick Mapper, then I would first suggest reading the official documentation, config.pdf, available in the doc folder of the Linux Joystick Mapper source code download.

Then you can take a look at these threads to see how to implement the joymap binary:

https://blog.petrockblock.com/forums/topic/mapping-a-game-controller-in-kodi/

https://retropie.org.uk/forum/topic/2032/dosbox-mapping-mouse-to-ps3-analog-stick

Once you've read these, I would suggest creating a simple mapper file that enters letters and numbers on a command line.

Ah. Sorry. I found this post with someone trying the same thing. They didn't come back to say if it worked or not though https://retropie.org.uk/forum/topic/5867/trying-to-make-two-bluetooth-controllers-act-as-player-1