@PaddyPat You might want to disable the ps3 controller driver and use the customhidsonly driver instead (you'll have to re-configure the controllers again after switching drivers).
Traditionally, Blueooth problems can be alleviated by disabling the Wifi or using a dedicated USB Bluetooth dongle - but for the 3B+ that may no longer be necessary since the wireless chips is better.

@meleu thanks so much for making this script! I would be screwed without it! This should be added to the Retropie main builds! It's so useful!

@hoover40 have you tried the RetroPie-joystick-selection tool?

It has not the exactly same flow as you described, but you can achieve what you want.

Link on my signature.