Thanks a lot Buzz for your reply!
I did as you said but that didn’t bring back that es_input.cfg / went with option #1 (binary-based installation) and the file was back. Had some pairing problems but solved that too with adding the lines into my /etc/init.d/rc.local file… But that was besides the initial problem.

But I still can not use the NES30 Pro in any emulator(s) – the file 8BitdoNES30Pro.cfg gets created under /opt/retropie/configs/all/retroarch-joypads but only the D-PAD works and the START is acting as the A-button… That’s it…

These are the relevant lines :

input_device = "8Bitdo NES30 Pro"
input_driver = "sdl2"
input_start_btn = "11"
input_a_btn = "0"
input_b_btn = "1"
input_x_btn = "3"
input_y_btn = "4"

Also added the contents of this cfg into the main retroarch.cfg (one level up) but no luck either…

On to more reading :)
/dimi