Thanks to others for posting their questions and answers. I ended up struggling with this one and doing a fair amount of Googlig to get a solution that verified. The tricky bit was not using the File System, so as others have pointed out creating a temporary file won't verify. For others that are still struggling the following code snippets might help. Extract zip file contents to byte arrays 
public static Map<String, byte[]> saveFilesInMap(ZipInputStream zipInputStream) {
    Map<String, byte[]> archiveContents = new HashMap<>();
    ZipEntry ze;
    try {
        while ((ze = zipInputStream.getNextEntry()) != null) {
            int len;
            byte[] buffer = new byte[1024];
            ByteArrayOutputStream baos = new ByteArrayOutputStream();
            while ((len = zipInputStream.read(buffer)) > 0) {
                baos.write(buffer, 0, len);
            }
            archiveContents.put(ze.getName(), baos.toByteArray());
            baos.close();
        }
    } catch (IOException e) {
        e.printStackTrace();
    }
    return archiveContents;
}
Save byte arrays to zip file 
public static void addByteArraysToArchive(Map<String, byte[]> byteArrays, ZipOutputStream zipOutputStream) {
    for (Map.Entry<String, byte[]> entry : byteArrays.entrySet()) {
        String name = entry.getKey();
        byte[] bytes = entry.getValue();
        try {
            ZipEntry zipEntry = new ZipEntry(name);
            zipEntry.setSize(bytes.length);
            zipOutputStream.putNextEntry(zipEntry);
            zipOutputStream.write(bytes);
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
}
Save file to zip file 
public static void addFileToArchive(String fileToBeAdded, ZipOutputStream zipOutputStream) {
    try {
        zipOutputStream.putNextEntry(new ZipEntry("new/" + Paths.get(fileToBeAdded).getFileName()));
        Files.copy(Paths.get(fileToBeAdded), zipOutputStream);
    } catch (IOException e) {
        e.printStackTrace();
    }
}