Maybe it will useful for other.
What you need is to put few line into batocera.conf (/userdata/system)
global.retroarch.input_shader_next_axis = "nul"
global.retroarch.input_shader_next_btn = "nul"
global.retroarch.input_shader_next_mbtn = "nul"
global.retroarch.input_shader_prev_axis = "nul"
global.retroarch.input_shader_prev_btn = "nul"
global.retroarch.input_shader_prev_mbtn = "nul"
it will disable switching shaders in-game with gamepad