Ok just tried what you suggested, heres what I did and the result.
System now boots up, I can access homebrew menu and run apps normally.
I cannot however boot any games, software won't launch and trying running Devmenu 6.x gives me a corruption error.
Do I need to downgrade to play my games? How do I go about getting this back to the way
You need patches put back in (I think) to play NSPs: https://gbatemp.net/threads/i-heard-that-you-guys-need-some-sweet-patches-for-atmosphere.521164/