How to merge two arrays by taking over only values from the second array that has the same keys as the first one?

This should do it, if I'm understanding your logic correctly:

array_intersect_key($changed, $filtered) + $filtered

---

Implementation:

$filtered = array(1 => 'a', 3 => 'c');
$changed = array(2 => 'b*', 3 => 'c*');
$expected = array(1 => 'a', 3 => 'c*');    
$actual = array_key_merge_deceze($filtered, $changed);

var_dump($expected, $actual);

function array_key_merge_deceze($filtered, $changed) {
    $merged = array_intersect_key($changed, $filtered) + $filtered;
    ksort($merged);
    return $merged;
}

Output:

Expected:
array(2) {
  [1]=>
  string(1) "a"
  [3]=>
  string(2) "c*"
}

Actual:
array(2) {
  [1]=>
  string(1) "a"
  [3]=>
  string(2) "c*"
}