I have found the way to get the values as I want them to be in the database. Changing the loop part in the above code with code did the trick.
$data = get_post_meta( get_the_ID(), 'combined', true );
foreach($data as $singleData => $value ){
$thisArray = $data[$singleData];
foreach ($thisArray as $key2 => $value){
add_post_meta( get_the_ID(), $singleData, $thisArray[$key2], $unique = false);
}
}