I finally gave up on the S.Bus converter. At first I thought that I could use it safely as long as I avoided using the AUX2 switch which seemed to be the main culprit in the loss of comms I was seeing but this passed week I almost lost or destroyed my Y6 when it went into failsafe and started climbing away. I never touched the AUX2 switch but it lost comms with just normal control stick inputs, I ended up cycling power on my TX and moving every knob and switch to somehow get control back and land the Y6.
Ive sinced moved to the DX6i TX I had lying around, I cant use the RTH functions but I can fly with it.