Script to convert old contao 2 src format to the new one by simply replacing the path with the id's. check comment in file for details.

Contao2srcTo3.php

<?php
/**
 * Copyright (c) 2013 Jean Bruenn
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */

/**
 * Requirenments:
 *  - PDO
 *  - Your database needs to support show tables and show columns from syntax. I've
 *    tested this script only with MySQL. 
 *
 * What does it do:
 * This script might be helpful for you, if you tried to convert your contao
 * installation (contao2) to contao3 and kept getting errors about your images
 * still beeing in contao2src format. This script iterates through every
 * table, looks for columns called singleSRC and multiSRC, checks for non-numeric
 * values within these fields and assume the fieldcontent needs to be
 * converted if found - hence it searches for the id of the file in tl_files and
 * updates the path accordingly.
 *
 * Due to this behaviour it is important that you synchronize your files before
 * running this script so it can find all files within tl_files.
 *
 * You might also want to run the following script first, which replaces occurences
 * of tl_files/ with files/
 *      https://gist.github.com/leofeyer/3304014
 *
 * Example Output:
 *     Retrieving a list of tables to convert...
 *     Found 6 tables with columns which might need to be converted...
 *     
 *     Converted 76 pictures (0 failed) in table tl_calendar_events
 *     Converted 0 pictures (0 failed) in table tl_content
 *     Converted 0 pictures (0 failed) in table tl_faq
 *     Converted 0 pictures (0 failed) in table tl_form_field
 *     Converted 73 pictures (0 failed) in table tl_module
 *     Converted 0 pictures (0 failed) in table tl_news
 * 
 *     Converted 149 pictures overall,
 *     couldn't convert 0 (did you synchronize files?) and
 *     failed to convert 0 files
 */
error_reporting(E_ALL ^ E_NOTICE);

$dbUser = '';
$dbData = '';
$dbPass = '';
$dbHost = '';

/**
 * @param $table
 * @param $db
 * @return bool
 */
function imageColumnsExist($table, $db)
{
    /**
     * I assume that a table which holds a column called
     * "singleSRC" and/or "multiSRC" needs to be converted.
     */
    $colres = $db->query("show columns from $table");
    while ($row = $colres->fetch(PDO::FETCH_NUM))
    {
        $columnName = $row[0];
        if (($columnName == 'singleSRC') || ($columnName == 'multiSRC'))
        {
            return true;
        }
    }

    return false;
}

/**
 * @param $path
 * @param $db
 * @return bool|int
 */
function findFileByPath($path, $db)
{
    /**
     * i had trouble using hash to find the file, hence using path.
     */
    $stmt = $db->query("SELECT id FROM tl_files WHERE path = '" . $path . "'");
    if ($stmt)
    {
        $row = $stmt->fetch();
        if ((isset($row['id'])) && (intval($row['id']) > 0))
        {
            return intval($row['id']);
        }
    }

    return false;
}

try
{
    $db  = new PDO('mysql:dbname=' . $dbData . ';host=' . $dbHost, $dbUser, $dbPass, array(PDO::MYSQL_ATTR_INIT_COMMAND => "SET NAMES 'UTF8'"));
    $res = $db->query("show tables");
    echo 'Retrieving a list of tables to convert...<br />';
    while ($row = $res->fetch(PDO::FETCH_NUM))
    {
        $tableName = $row[0];
        if (substr($tableName, 0, 3) == 'tl_')
        {
            if (imageColumnsExist($tableName, $db))
            {
                $tables[] = $tableName;
            }
        }
    }
    echo 'Found ' . count($tables) . ' tables with columns which might need to be converted...<br /><br />';

    $converted   = 0;
    $missingFile = 0;
    $failed      = 0;
    foreach ($tables as $tableName)
    {
        $tableConverted = 0;
        $tableFailed    = 0;
        $stmt           = $db->query("SELECT * FROM $tableName");
        while ($row = $stmt->fetch(PDO::FETCH_ASSOC))
        {
            if ((isset($row['singleSRC'])) && (!empty($row['singleSRC'])) && (!is_numeric($row['singleSRC'])))
            {
                if ($newId = findFileByPath($row['singleSRC'], $db))
                {
                    $update = $db->exec("UPDATE $tableName SET singleSRC = $newId WHERE id = '" . $row['id'] . "'");
                    if ($update > 0)
                    {
                        $tableConverted++;
                    } else
                    {
                        $tableFailed++;
                    }
                } else
                {
                    $missingFile++;
                }
            }
            if ((isset($row['multiSRC'])) && (!empty($row['multiSRC'])))
            {
                $pictureList = unserialize($row['multiSRC']);
                if (is_array($pictureList))
                {
                    foreach ($pictureList as $picture)
                    {
                        if (!empty($picture) && (!is_numeric($picture)))
                        {
                            if ($newId = findFileByPath($picture, $db))
                            {
                                $multiSRC[] = $newId;
                                $tableConverted++;
                            } else
                            {
                                $missingFile++;
                            }
                        }
                    }
                }
                if ((isset($multiSRC)) && (count($multiSRC) > 0))
                {
                    $multiSRCstr = serialize($multiSRC);
                    $update      = $db->exec("UPDATE $tableName SET multiSRC = '" . $multiSRCstr . "' WHERE id = '" . $row['id'] . "'");
                    if ($update <= 0)
                    {
                        $tableFailed++;
                    }

                    unset($multiSRC);
                }

            }

        }
        $converted += $tableConverted;
        $failed += $tableFailed;
        echo "Converted $tableConverted pictures ($tableFailed failed) in table $tableName<br />";
    }
    echo "<br />Converted $converted pictures overall,<br />couldn't convert $missingFile (did you synchronize files?) and<br />failed to convert $failed files<br />";
} catch (PDOException $e)
{
    echo $e->getMessage();
}