You have now:

  employee.addComputer(computer);
        pm.close();

Replace with:

  employee.addComputer(computer);
  pm.makePersistent(employee);
  pm.close();

You update entity but don't persist it again.

Also replace:

  @Persistent
    public Set<Long> computerKeys = new HashSet<Long>();

with:

    @Persistent(defaultFetchGroup = "true")
    public Set<Long> computerKeys = new HashSet<Long>();

I'm not sure if method: "employeeCheck.computerKeys.isEmpty())"
launches "lazy loading".
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