Upgrading a RTE-enabled field from a custom table with a RTE to FAL. Note that this is keyed to a particular upload path (old and new). Change the class constants to your needs.

gistfile1.php

<?php
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*  (c) 2013 Francois Suter <typo3@cobweb.ch>
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/**
 * Class for updating images in RTE field
 *
 * @author		Francois Suter <typo3@cobweb.ch>
 * @package		TYPO3
 * @subpackage	tx_latourdoctors
 */
class ext_update {
	const ORIGINAL_DIRECTORY = 'uploads/tx_latourdoctors/rte/';
	const TARGET_DIRECTORY = '/_migrated/RTE/latourdoctors/';

	/**
	 * The default storage
	 * @var \TYPO3\CMS\Core\Resource\ResourceStorage
	 */
	protected $storage;

	/**
	 * Performs the updates of RTE images to FAL, based on existing references
	 *
	 * @return string Result of the migration script
	 */
	public function main() {
		$customMessages = '';
		$queries = array();

		// Initialize the storage repository
		/** @var $storageRepository \TYPO3\CMS\Core\Resource\StorageRepository */
		$storageRepository = \TYPO3\CMS\Core\Utility\GeneralUtility::makeInstance('TYPO3\\CMS\\Core\\Resource\\StorageRepository');
		$storages = $storageRepository->findAll();
		$this->storage = $storages[0];
		/** @var $fileRepository \TYPO3\CMS\Core\Resource\FileRepository */
		$fileRepository = \TYPO3\CMS\Core\Utility\GeneralUtility::makeInstance('TYPO3\\CMS\\Core\\Resource\\FileRepository');

		// Create the directory, if necessary
		$fileadminDirectory = rtrim($GLOBALS['TYPO3_CONF_VARS']['BE']['fileadminDir'], '/');
		$targetDirectory = self::TARGET_DIRECTORY;
		$targetFolder = $this->storage->createFolder($targetDirectory);

		// Perform update by looping on all existing references
		$oldRecords = $this->findMagicImagesInOldLocation();
		foreach ($oldRecords as $refRecord) {

			// is usually uploads/RTE_magicC_123423324.png.png
			$sourceFileName     = $refRecord['ref_string'];
			// absolute path/filename
			$fullSourceFileName = PATH_site . $refRecord['ref_string'];
			$targetFileName     = $targetDirectory . \TYPO3\CMS\Core\Utility\PathUtility::basename($refRecord['ref_string']);

			// if the source file does not exist, we should just continue, but leave a message in the docs;
			// ideally, the user would be informed after the update as well.
			if (!file_exists(PATH_site . $sourceFileName)) {

				$format = 'File \'%s\' does not exist. Referencing field: %s.%d.%s. The reference was not migrated.';
				$message = \TYPO3\CMS\Core\Utility\GeneralUtility::makeInstance('\TYPO3\CMS\Core\Messaging\FlashMessage',
					sprintf($format, $sourceFileName, $refRecord['tablename'], $refRecord['recuid'], $refRecord['field']),
					'', \TYPO3\CMS\Core\Messaging\FlashMessage::WARNING
				);
				/** @var \TYPO3\CMS\Core\Messaging\FlashMessage $message */
				$customMessages .= '<br />' . $message->render();

				continue;
			}

			// Check if the file is already known by FAL, if not add it
			$file = $this->storage->getFile($targetFileName);
			if (!($file instanceof \TYPO3\CMS\Core\Resource\File)) {
				// Move the file to the storage and index it (indexing creates the sys_file entry)
				$file = $this->storage->addFile($fullSourceFileName, $targetFolder);
				$fileRepository->addToIndex($file);
			}

			if ($file instanceof \TYPO3\CMS\Core\Resource\File) {
				// and now update the referencing field
				$targetFieldName = $refRecord['field'];
				$targetRecord = $GLOBALS['TYPO3_DB']->exec_SELECTgetSingleRow(
					'uid, ' . $targetFieldName,
					$refRecord['tablename'],
					'uid = ' . intval($refRecord['recuid'])
				);
				if ($targetRecord) {
					// replace the old filename with the new one, and update the corresponding record
					$targetRecord[$targetFieldName] = str_replace($sourceFileName, $fileadminDirectory . $targetFileName, $targetRecord[$targetFieldName]);
					$GLOBALS['TYPO3_DB']->exec_UPDATEquery(
						$refRecord['tablename'],
						'uid = ' . intval($refRecord['recuid']),
						array($targetFieldName => $targetRecord[$targetFieldName])
					);
					$queries[] = str_replace(LF, ' ', $GLOBALS['TYPO3_DB']->debug_lastBuiltQuery);

					// finally, update the sys_refindex table as well
					$GLOBALS['TYPO3_DB']->exec_UPDATEquery(
						'sys_refindex',
						'hash = ' . $GLOBALS['TYPO3_DB']->fullQuoteStr($refRecord['hash'], 'sys_refindex'),
						array(
							'ref_table'  => 'sys_file',
							'ref_uid'    => $file->getUid(),
							'ref_string' => $fileadminDirectory . $targetFileName
						)
					);
					$queries[] = str_replace(LF, ' ', $GLOBALS['TYPO3_DB']->debug_lastBuiltQuery);
				}

			}
		}
		$content = '';
		// Display only the count of queries (and not all the queries, since that may be a lot, and containing much
		// content too.
		if (count($queries) > 0) {
			$content .= sprintf('%d queries were performed', count($queries));
		}
		$content .= '<hr>' . $customMessages;
		return $content;
	}

	/**
	 * Go through the soft refindex and find all occurrences where the old filename
	 * is still written in the ref_string
	 *
	 * @return array Entries from sys_refindex
	 */
	protected function findMagicImagesInOldLocation() {
		$records = $GLOBALS['TYPO3_DB']->exec_SELECTgetRows(
			'hash, tablename, recuid, field, ref_table, ref_uid, ref_string',
			'sys_refindex',
			'ref_string LIKE "' . $GLOBALS['TYPO3_DB']->escapeStrForLike(self::ORIGINAL_DIRECTORY, 'sys_refindex') . '%"',
			'',
			'ref_string ASC'
		);
		return $records;
	}

	/**
	 * Is update needed? Always TRUE
	 *
	 * @param string $what
	 * @return bool
	 */
	public function access($what = 'all') {
		return TRUE;
	}
}
?>