Update:
After a fresh install of 7.2, and my 8bitdo controllers work fine in B_Start mode in the main menu's but when I go to any game I have to turn off the controllers and then turn them on again to pair them. After that they will work in the games. The Hotkey does cycle through the shaders. I found an almost identical issue in the forums for version 7.0.1.

https://forum.recalbox.com/topic/22222/7-0-1-controller-works-in-emulationstation-but-not-in-retroarch

@lhari84

I am new to all of this, is there a place I can download version 7.1.1 again. I dont have a backup of it that I know of. I will for the versions in the future.

I am having the same issue, I updated this afternoon and now none of my controllers work. Is there any way to go back to 7.1.1?