int batchSize = 100, count = 0;

User currentUser = null, lastUser = null;
           
ScrollableResults users =
session.getNamedQuery("User.findAllForRanking")
       .setCacheMode(CacheMode.IGNORE)
       .setFlushMode(FlushMode.MANUAL)
       .scroll(ScrollMode.FORWARD_ONLY);
           
while (users.next()) {
    // Don't run this the first time, since currentUser will be null
    // The other times through the loop, the current user needs to be
    // re-attached to the persistence context since it was evicted when
    // the batch was flushed, but that one User object is still needed.
    if (count > 0)
        lastUser = (count % batchSize == 0) ? (User)session.merge(currentUser) : currentUser;

    currentUser = (User)users.get(0);
               
    count++;

    //...
    //Adjust the user's global ranking, basically just user.setCurrentRanking(x);
    //...

    if (count % batchSize == 0) {
        session.flush(); // PROBLEM HAPPENS HERE
        session.clear();
    }
}
           
// Flush it once more, in case there were any unflushed entities at
// the end of the loop execution
session.flush();
session.clear();
           
// Close the ScrollableResults
users.close();