How to correctly export all Box files for a user using JWT service account

Using a JWT service account I want to access all Box.com files for User with ID 234234 and login nick.jackson

So I create a jwt api connection:

String privateKey = new String(Files.readAllBytes(Paths.get(boxJwtPrivateKeyFile)));

JWTEncryptionPreferences encryptionPref = new JWTEncryptionPreferences();
encryptionPref.setPublicKeyID(boxJwtPublicKeyId);
encryptionPref.setPrivateKey(privateKey);
encryptionPref.setPrivateKeyPassword(boxJwtPrivateKeyPassword);
encryptionPref.setEncryptionAlgorithm(EncryptionAlgorithm.RSA_SHA_256);

IAccessTokenCache accessTokenCache = new InMemoryLRUAccessTokenCache(MAX_CACHE_ENTRIES);

api = BoxDeveloperEditionAPIConnection.getAppUserConnection(boxAppUserId, apiKey, apiSecret,
      encryptionPref, accessTokenCache);

Then I set the As-User header as 234234

api.setRequestInterceptor((RequestInterceptor) request -> {
  request.addHeader("As-User", "234234");
// Returning null means the request will be sent along with our new header.
  return null;
});

Does this get all files owned by this user? It definitely also includes files shared to the user or available through group/user membership to a directory.

One problem - I see situations where I find files from one owner in one As-User, then when I go look for them as that user itself in As-User I don't find them. Why is that? 

Example:

As-User=234234

  -> has file 58583532 owned by 345525

As-User=345525

  -> Don't have that file 58583532

Am I doing anything wrong?