I was able to get Hotkeys working with my GPIO Controls acting as keyboard.
cd /opt/retropie/configs/all $ sudo nano retroarch.cfg
input_player1_l = “l”
input_player1_r = “r”
input_hold_fast_forward = “nul”
input_rewind = “nul”
input_enable_hotkey = “v”
input_load_state = “l”
input_save_state = “r”
I added the above code. By default the l and r were used for FastForward and Rewind. So making them nul and adding the hotkey command to v which is what one of my buttons maps to enabled that. The only thing that it affected that I wasn’t expecting was the button I had mapped as Esc no longer worked without the Hotkey being used. Other than that, works like a boss! Hope it helps.