Demonstrate possible bug with PDO. The following does not work, but does if you replace `$database->query` with prepared statements.

demonstration.php

<?php

/**
 * Perform a cleanup that spans multiple tables and columns
 * 
 * @param string $dir The directory to search. This should be
 * a relative directory starting with "upload/", e.g. 
 * "upload/galleries/". The trailing slash is required.
 * @param PDO $database The database object to use
 * @param string[][] $searchArray An array of arrays of exactly 
 * 2 strings. The first string is the table name, and the second 
 * is the column name.
 */
function tableFileCleanupMulti($dir, $database, $searchArray){
    // First we need to build an SQL query to get all the 
    // images in the given search array
    echo '<hr style="margin-top: 30px;"/><h2>'.$dir.'</h2>';
    $matchString = $database->quote("%$dir%");
    $sql = implode(' UNION ', array_map(function($tableAndCol) use ($matchString){
        $table = $tableAndCol[0];
        $column = $tableAndCol[1];
        return "SELECT $column FROM $table WHERE $column LIKE $matchString";
    }, $searchArray));
    
    $result = $database->query($sql, PDO::FETCH_COLUMN);
    // Now we need to extract all paths from the data we got
    $foundFiles = [];
    $regex = "|{$dir}[-A-Za-z0-9_.]+|";
    
    foreach ($result as $textBlock){
        $matches = [];
        preg_match_all($regex, $textBlock, $matches);
        array_push($foundFiles, ...$matches[0]);
    }
    
    foreach (scandir($dir) as $file) {
        if ('.' === $file) continue;
        if ('..' === $file) continue;

        if (!in_array($dir.$file, $foundFiles)){
            // delete files not in the database
            echo '<br/>Deleting file: '.$dir.$file;
            deleteFile($dir.$file);
        }
        else{
            echo '<br/>Keeping file: '.$dir.$file;
        }
    }
}

tableFileCleanupMulti('upload/imgs/', $DATABASE, [
    ['settings', 'value'],
    ['articles', 'content'],
])
  
?>