You can do it with using a FileOutputStream and the writeTo method.

ByteArrayOutputStream byteArrayOutputStream = getByteStreamMethod();
try(OutputStream outputStream = new FileOutputStream("thefilename")) {
    byteArrayOutputStream.writeTo(outputStream);
}

Source: "Creating a file from ByteArrayOutputStream in Java." on Code Inventions

Hmm,

        zipSubDirectory(path, file, zout);
        zout.closeEntry();

should be:

        zout.closeEntry();
        zipSubDirectory(path, file, zout);

The main error seems to be that zout is not closed / flushed before toByteArray is called. Here try-with-resources was a bit devious.

try (ByteArrayOutputStream bos = new ByteArrayOutputStream()) {
    try ((ZipOutputStream zout = new ZipOutputStream(bos)) {
        zipSubDirectory("", dir, zout);
    }
    return bos.toByteArray();
} catch (IOException e) {
    throw new RuntimeException(e);
}