Use MKVMerge and Handbrake to check every video file in a directory and its subdirectories for the proper audio encoding for playback on a Chromecast and transcode it if it does not.

chromecast_audio.php

<?php
    // This is going to take a while
    set_time_limit(0);

    /**
     * Path to MKVMerge executable
     */
    $mkvmerge = 'mkvmerge.exe';
    /**
     * Path to HandbrakeCLI executable
     */
    $handbrakeCLI = 'HandbrakeCLI.exe';
    /**
     * Directory to search for files to convert in
     */
    $directory = 'MOVIES';
    /**
     * Extensions of files to check
     */
    $extensions = array('mkv','mp4');
    /**
     * Audio encodings supported by Chromecast
     */
    $allowed = array('AAC', 'MP3');
    
    // Create recursive iterator for all files in the provided directory and its subdirectories
    $di = new RecursiveDirectoryIterator(
        $directory, 
        (FilesystemIterator::KEY_AS_PATHNAME | FilesystemIterator::CURRENT_AS_FILEINFO | FilesystemIterator::SKIP_DOTS)
    );
    $di = new RecursiveIteratorIterator($di);
    
    // Use MKVMerge to check if each file has the proper audio encoding
    echo "Searching directory...\n";
    $toTranscode = array();
    foreach($di as $file) {
        if(in_array(strtolower($file->getExtension()), $extensions)){
            $path = $di->getRealPath();
            $output = shell_exec("$mkvmerge -i $path\n");
            if(preg_match_all('/audio \((.+)\)/i', $output, $matches)){
                if(!count(array_intersect($allowed, $matches[1]))){
                    $toTranscode[] = $path;
                    echo "Added \"$file\" to transcoding queue\n";
                }
            }
        }
    }
    
    echo 'Press enter to start transcoding...';
    if(stream_get_line(STDIN, 1) === false){
        exit;
    }

    // Transcode each file in the queue. See HandbrakeCLI documentation for explanation of arguments
    echo "Starting transcoding queue...\n";
    foreach($toTranscode as $file) {
        echo "Transcoding \"$file\"...\n";
        passthru("$handbrakeCLI -f mkv --preset \"AppleTV 3\" -i \"$file\" -o \"$file.tmp\"");
    }
    

?>