<?php
$valoresStr = '500038;204932
500038;204932
100398;204932
100398;204932
100398;204932
100398;204932';

$arrayTemp = explode(chr(10), trim($valoresStr));

$arrayValores = array_count_values($arrayTemp);

var_dump($arrayValores);

foreach ($arrayValores as $valor => $soma) {
    $valoresStr = str_replace($valor, $soma . ';' . $valor, $valoresStr);
}

echo PHP_EOL;

echo $valoresStr;