Student or Learner
The parts were / had shipped with the goods on 02 June.
The parts had been shipped with the goods on 02 June by John.
John had shipped the parts along with the goods on 02 June.
The first sentence is a passive voice. There you use "had been" in this context.
Note: There are many other rules to use "had been". The above is just an example to describe this situation about the use of "had" and "had been".
May be an expert could add more value to it.