Ok, I have also got it working again but I didn’t get any notifications.
I just reinstalled MSI Center without Mystic Light and the motherboard reappeared in SignalRGB devices after restarting app, no warnings about conflicting software at all, yet!
Update:
I spoke way too soon, I tried to open MSI Center and immediately got the conflicting application warning again, but everything worked again after using the msi removal tool.
Wow, what a palaver.