I'm having the almost same issue described here.
I'm using iMac 27 2019 and Magic Trackpad 2 and Kensington Slimblade trackball (wired connection) and Logitech Mx Master 2s (wireless or bluetooth connection).
What occasionally happens is that both Kensington Slimblade and MX master 2s (both) stop scrolling.
(It happens 'globally;' it's not an app-specific problem.)
In order to make them scroll again,
I have to restart BTT or scroll a little bit on the trackpad.
I'm having this issue both on Mojave and Catalina.
I've been trying changing various settings in BTT, but nothing helps.
When I turn off BTT, this problem never occurs.
It seems that something in BTT prevents scroll input from other devices other than Magic Trackpad 2,
but I'm not sure what's really happening.