Missing updates with locks and ConcurrentHashMap
The answer provided by @Slaw in the comments did the trick. We were letting the instrumentList instance escape in non-synchronized way i.e. access/operations are happening over list without any synchonization. Fixing the same by passing the copy to further methods did the trick.
Following line of code is the one where this issue was happening
Here we are allowing the instrumentList instance to escape in non-synchronized way i.e. it is passed to another class (recordSaver.persist) where it was to be actioned on but we are also clearing the list in very next line(in Aggregator class) and all of this is happening in non-synchronized way. List state can't be predicted in record saver... a really stupid mistake.
We fixed the issue by passing a cloned copy of instrumentList to recordSaver.persist(...) method. In this way instrumentList.clear() has no affect on list available in recordSaver for further operations.