Another approach is that You can create and Use some session variable to achieve it easily.
E.g. $_SESSION['validate']. 
HTML and PHP Code for buttons
<button type="submit" id="first_submit" style="<?php echo isset($_SESSION['validate'])?'display:none':'';?>">first submit</button>
<button type="submit" id="second_submit" style="<?php echo isset($_SESSION['validate'])?'':'display:none';?>">second submit</button>
jquery and ajax Script
<script>
    $(document).ready(function(){
        $("#form").on('submit', function(e){
            e.preventDefault();
            $.ajax({
                type: 'POST',
                url: 'handler-file.php',
                data:  new FormData(this),
                dataType: "json",
                enctype: 'multipart/form-data',
                contentType: false,
                cache: false,
                processData:false,
                error:function(error){
                    //your required code or alert
                    alert(error.responseText);
                },
                success: function(response){
                    if(response.status=='1')
                    {
                        //your required code or alert
                        $('#first_submit').hide();
                        $('#second_submit').show();
                    }
                    else if(response.status=='2')
                    {
                        //your required code or alert
                        $('#first_submit').show();
                        $('#second_submit').hide();
                    }
                    else
                    {
                        //your required code or alert
                    }
                }
            });
        });
    });
    </script>
Handler PHP File
<?php
session_start();
$result['status']='0';
$result['error']='';
if(!isset($_SESSION['validate']))
{
    if(!isset($_FILES['file'])) 
    {
        $result['error'].='[Er-02 file missing!]';
    }
    else
    {
        //your other code
        $_SESSION['validate'] = true;
        $result['status']='1';
    }
}
else if($_SESSION['validate']==true)
{
    if(!isset($_FILES['file'])) 
    {
        $result['error'].='[Er-03 Validation file missing!]';
    }
    else
    {
        //your other code
        unset($_SESSION['validate']);
        $result['status']='2';
    }
}
else
{
    $result['error'].='[Er-01 Invalid source!]';
}
echo json_encode($result); 
?>
It may not be the optimal or efficient solution. My level of experience is not too much, so I came up with this solution what served my purpose best after all the solutions available but with their limitations. This was not anywhere so thought to write it here.
Note: You may notice it includes some other parts like response, success and error handling between presentation, script and backend file.
Hope it helps!