How can I write file without overwrite

I'm trying to store my settings, but I can't well. I have too much variable.I have settings[variable] input I use this at form inputs.
Like this;

Form1 has these inputs

PHP Code:

<input type="text" class="form-control" name="settings[facebook]">
<input type="text" class="form-control" name="settings[twitter]">
<input type="text" class="form-control" name="settings[site_title]">
<input type="text" class="form-control" name="settings[site_description]">
<input type="text" class="form-control" name="settings[site_keywords]"> 


Form2 has these inputs

PHP Code:

<input type="text" class="form-control" name="settings[jumboH1]">
<input type="text" class="form-control" name="settings[jumboParagraph]">
<input type="text" class="form-control" name="settings[panel1]">
<input type="text" class="form-control" name="settings[panel2]">
<input type="text" class="form-control" name="settings[panel3]"> 


And i post these with a hidden input at this controller. It is a method:
This method apply settings.php incoming settings[] array but removing all of settings.php and write again.

PHP Code:

public function applysetting()
    {
        $submit = $this->input->post('submit');
        if (isset($submit)) {
            $html = '<?php' . PHP_EOL . PHP_EOL;
            foreach ($this->input->post('settings') as $key => $value) {
                $html .= '$settings["' . $key . '"]="' . $value . '";' . PHP_EOL;
            }
            file_put_contents(FCPATH . '/settings.php', $html);
        }
    } 


If i replace file_put_contents to write_file(FCPATH . '/settings.php', $html, 'a') it rewrites the same things. For example

PHP Code:

<?php

$settings["jumboH1"]="Login h1 test";
$settings["jumboParag"]="Login paragraph test";
$settings["panel1"]="Panel 1";
$settings["panel2"]="Panel 2";
$settings["panel3"]="Panel 3";
<?php

$settings["jumboH1"]="input1";
$settings["jumboParag"]="input2";
$settings["panel1"]="input3";
$settings["panel2"]="input4";
$settings["panel3"]="input5";

<?php

[size=small][font=Monaco, Consolas, Courier, monospace]$settings["jumboH1"]="input test";[/font][/size]
[size=small][font=Monaco, Consolas, Courier, monospace]$settings["jumboParag"]="input test2";[/font][/size]
[size=small][font=Monaco, Consolas, Courier, monospace]$settings["panel1"]="input333";[/font][/size]
[size=small][font=Monaco, Consolas, Courier, monospace]$settings["panel2"]="input444";[/font][/size]
$settings["panel3"]="input115"; 


How can i fix it?