Hi,
  One  possibility is to set IgnoreChanges [1] to true.

  Other possibility is Application A is serving data from QueryCache [1].
  Try disabling it explicitly.
  
  The third (more drastic) is to call em.clear() before querying in
Application A.

[1]
http://openjpa.apache.org/builds/latest/docs/manual/manual.html#openjpa.IgnoreChanges
[2]
http://openjpa.apache.org/builds/latest/docs/manual/manual.html#ref_guide_cache_query

Pinaki

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