public WriteDecodedDoc() 
{
        super();
}

Constructor.

 public  void doIt(String in,
    String out) throws IOException, COSVisitorException 
{
        PDDocument doc = null;
        try
        {
            doc = PDDocument.load( in );
            if( doc.isEncrypted() )
            {
                try
                {
                    doc.decrypt( "" );
                }
                catch( InvalidPasswordException e )
                {
                    System.err.println( "Error: The document is encrypted." );
                }
                catch( org.apache.pdfbox.exceptions.CryptographyException e )
                {
                    e.printStackTrace();
                }
            }
            for (Iterator i = doc.getDocument().getObjects().iterator(); i.hasNext();)
            {
                COSBase base = ((COSObject) i.next()).getObject();
                if (base instanceof COSStream)
                {
                    // just kill the filters
                    COSStream cosStream = (COSStream)base;
                    cosStream.getUnfilteredStream();
                    cosStream.setFilters(null);
                }
            }
            doc.save( out );
        }
        finally
        {
            if( doc != null )
            {
                doc.close();
            }
        }
}

This will perform the document reading, decoding and writing.

 public static  void main(String[] args) 
{
        WriteDecodedDoc app = new WriteDecodedDoc();
        try
        {
            if( args.length != 2 )
            {
                app.usage();
            }
            else
            {
                app.doIt( args[0], args[1]);
            }
        }
        catch (Exception e)
        {
            e.printStackTrace();
        }
}

This will write a PDF document with completely decoded streams.
see usage() for commandline