@muldjord
Just downloaded the script, is there anything you can see here that would mess things up?
#!/bin/bash
pushd /home/pi/
wget https://github.com/HoraceAndTheSpider/RetroPieAmigaSetup/archive/master.zip
unzip master.zip
rm master.zip
mv RetroPieAmigaSetup-master .retropie_amiga_setup
cd .retropie_amiga_setup
python3 amiga_setup_script.py
cd ..
rm -r .retropie_amiga_setup
cp /home/pi/RetroPie/BIOS/Amiga/kick13.rom /home/pi/RetroPie/roms/amiga-data/_BootWHD/Devs/Kickstarts/kick34005.A500
cp /home/pi/RetroPie/BIOS/Amiga/kick31.rom /home/pi/RetroPie/roms/amiga-data/_BootWHD/Devs/Kickstarts/kick40068.A1200
cp /home/pi/RetroPie/BIOS/Amiga/kick12.rom /home/pi/RetroPie/roms/amiga-data/_BootWHD/Devs/Kickstarts/kick33180.A500
popd
I have checked the cp entries and all the relevant rom files I extracted from the other image are in that folder anyway so I wouldn't think that part would be an issue..
UPDATE: Looking at that script and digging through I've found a RetroPieAmigaSetup-master.zip and a UAEConfigMaker-master.zip downloaded and scripts contained within were executed. I'll dig through those and see if there anything that has moved/re-routed something