The serialization of the NestedJarFromStream is incorrect. Its using default serialization of these fields:

private transient ZipInputStream zis;
private URL jarURL;
private URL entryURL;
private long lastModified;
private long size;
private AtomicBoolean inited = new AtomicBoolean(false);

The problem is that the inited flag should not be serialized as this implies its parents fields:

private transient List<VirtualFileHandler> entries;
private transient Map<String, VirtualFileHandler> entryMap;

have been initialized. They will not be after deserialization of NestedJarFromStream as it lazily does initialization.