Deleting that file is not advisable, since it contains more than your input configuration. Either restore it from a backup (there should be a es_input.cfg.bak you can use) or re-install the EmulationStation package.
Once you have the .cfg file recovered, re-configure your I-PAC2 in EmulationStation and the configuration for RetroArch and other emulators should be created.

@tuki_cat

And thanks again, I succesfully mapped the 1 to F1, 2 to F3 and 5 to F5. Although it required some steps.

First I mapped (as you told above) with the virtual keyboard the correct keys, and then saved it. After restarting the Vice emulator the keys weren't mapped anymore. When I loaded the keymap again the keys still didn't work. Then I thought maybe I can add the changed keys in the dsl-vicerc file (a bit like the F12 file) but then more like this "49 0 4 9" which is 1 to F1. That didn't work but I noticed that it would load the keymap according thje dsl-vicerc file, but somehow that didn't work.

Looking in the vice.log file I noticed that it says: Loading keymap `/opt/retropie/emulators/vice/lib/vice/C64/sdl_sym.vkm'
Now I wen to that file changed it according to the saved keymap and it works. Strange thing is that is doesn't look at the keymap it should load.

And what I did for the Dosbox is create .sh file. Not sure if it works for C64 but you can try this e.g:

roms\c64\frogger.sh

sc c64/frogger/keymap.vkm /opt/retropie/emulators/vice/lib/vice/C64/sdl_sym.vkm load frogger\frogger.crt

The problem is I don't know if there is a command to go from the .sh file to the crt/tap/etc file. Don't think 'load' wil do the trick haha.

@max209 said in ES recognizes controlls but games with retroarch won't:

But sometimes when i install a different image, like retropie for the odroid XU4 or a modded image for the Pi 3 (not every), the controls are being recognized in ES and i can appoint them in retroarch (main menu retropie) but within games they wont work at all.

I'm afraid we don't support these custom images. the only ones we support are these: https://retropie.org.uk/download/