<?php
$one = array('start' => '2012-10-12', 'stop' => '2012-11-04', 'over' => false);
$two = array('start' => '2012-10-29', 'stop' => '2012-11-14', 'over' => true);
$three = array('start' => '2012-11-12', 'stop' => '2012-12-07', 'over' => false);

$arr = array($one, $two, $three);

foreach($arr as $key=>$val)
{
   if(isset($arr[$key+1]) && $arr[$key+1]['over'] == true)
       $arr[$key]['stop'] = date('Y-m-d', strtotime($arr[$key+1]['start'] .' -1 day'));
  if(isset($arr[$key-1]) && $arr[$key-1]['over'] == true)
       $arr[$key]['start'] = date('Y-m-d', strtotime($arr[$key-1]['stop'] .' +1 day'));
}

var_dump($arr);
?>

array(3) {
  [0]=>
  array(3) {
    ["start"]=>
    string(10) "2012-10-12"
    ["stop"]=>
    string(10) "2012-10-28"
    ["over"]=>
    bool(false)
  }
  [1]=>
  array(3) {
    ["start"]=>
    string(10) "2012-10-29"
    ["stop"]=>
    string(10) "2012-11-14"
    ["over"]=>
    bool(true)
  }
  [2]=>
  array(3) {
    ["start"]=>
    string(10) "2012-11-15"
    ["stop"]=>
    string(10) "2012-12-07"
    ["over"]=>
    bool(false)
  }
}