Hey i ran into trouble with the emulatorstation and uae4rpi too and i think it belongs here.
I am able to run games by manually creating the symbolic link to ad0.adf and running ./uae4all
But if i try to run one of the games in emulatorstation only the amiga screen that asks for the disks appears.
I made some investigation and wondered why the symbolic link does not direct to the rom at all but only to the folder /home/pi/Retropie/roms/
The /opt/retropie/emulators/uae4rpi/startAmigaDisk.sh creates the symbolic link with ln -s "/home/pi/RetroPie/roms/amiga/" "df0.adf"
This explains the wrong symbolic link but altering the script like this doesn’t help too. ln -s "/home/pi/RetroPie/roms/amiga/$1" "df0.adf"
For me it seems as if the station does not pass the filename.
I am not very experienced with linux so i hope you can help me out or determine if its a bug.