I remember having an issue before with Amiberry and trying to reset the autoboots of my games. If I remember correctly I fixed it by going to:
/opt/retropie/configs/amiga/amiberry/whdboot/game-data
And deleting the whdload_db.xml file from there (or you could manually go through the entire list and remove the entries you wish to show the bootloader for again).
Obviously I would strongly suggest backing up the file first before deleting or editing it! I hope this helps!
