Was editing my map presets and testing them out when I somehow managed to have the cave settings to be the same as the overworld settings minus the season settings. All cave entrances go to a different map so there is two overworld maps and no caves. It works the opposite way too so it's quite interesting.
Set the caves as a numbered custom preset then go on the overworld settings and overwrite the custom preset the caves are set to and then generate the world. It works the opposite way too and can have a dual cave world.