Así es como tenía consistente el catálogo de iTunes antes de conocer http://dougscripts.com/itunes/

CheckItunesLibrary.java

import com.sun.org.apache.bcel.internal.classfile.JavaClass;
import java.util.Arrays;
import javax.xml.xpath.*;
import java.io.File;
import java.io.FileInputStream;
import org.xml.sax.InputSource;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import java.util.HashSet;
import java.net.URLDecoder;

public class CheckItunesLibrary {
    
    static HashSet<String> setItunes = new HashSet<String>();
    static HashSet<String> setFiles = new HashSet<String>();
    static float sizeOrphanFiles;
    
    public static void main(String[] args) {
        try {
            String iTunesLibraryPath = null;
            String iTunesCatalogPath = null;

            if (args.length==0) usage();
            
            // Parse arguments
            if (args[0].equals("-usage")) {
                usage();
            } else if (args[0].equals("-help")) {
                usage();
            } else {
                if (args.length!=2) usage();
                iTunesLibraryPath = args[0];
                iTunesCatalogPath = args[1];
            }
            XPathFactory factory = XPathFactory.newInstance();
            XPath xPath = factory.newXPath();
            File xmlDocument = new File(iTunesCatalogPath);
            InputSource inputSource =  new InputSource(new FileInputStream(xmlDocument));
            String expression = "/child::plist/child::dict/child::dict/child::dict/child::key[text()='Location']/following-sibling::string/child::text()";
            NodeList nodes = (NodeList) xPath.evaluate(expression, inputSource, XPathConstants.NODESET);
            for (int i = 0; i < nodes.getLength(); i++) {
                String path = URLDecoder.decode(nodes.item(i).getNodeValue(),"UTF-8");
                setItunes.add(parseFilePath(path));
            }
            File f = new File(iTunesLibraryPath);
            checkFiles(f);
            System.out.println(setItunes.size() + " missing files");
            System.out.println(join(setItunes.toArray(new String[1]),"\n"));
            System.out.println(setFiles.size() + " orphan files (" + sizeOrphanFiles + " MB)");
            System.out.println(join(setFiles.toArray(new String[1]),"\n"));
        } catch (Exception e) {
            System.out.println("MESSAGE:\t" + e.getMessage());
            System.out.println("STACK:\t" + Arrays.toString(e.getStackTrace()));
            e.printStackTrace();
        }
    }

    private static void usage() {
        System.err.println("Usage: CheckItunesLibrary <libraryPath> <catalogPath>");
        System.err.println("       -usage or -help = this message");
        System.exit(1);
    }
    
    private static String parseFilePath(String path) {
        if (File.separatorChar != '/') {
            path = path.replace(File.separatorChar, '/');
        }
        return path;
    }
    
    private static void checkFiles(File f) {
        if (f.isDirectory()) {
            File[] files = f.listFiles();
            for (File file: files) {
                if (file.isDirectory())
                    checkFiles(file);
                else
                    checkFile(file);
            }
        }
        else
            checkFile(f);
    }
    
    private static void checkFile(File f) {
        if (!setItunes.remove(parseFilePath(f.getAbsolutePath()))) {
            setFiles.add(parseFilePath(f.getAbsolutePath()));
            sizeOrphanFiles += f.length() / (1024*1024);
        }
    }
    
    private static String join(String[] strings, String separator) {
        StringBuffer sb = new StringBuffer();
        for (String s: strings) {
            sb.append(s);
            sb.append(separator);
        }
        return sb.toString();
    }
}