Had/has/have been is usually used for something that was done in the past and still applies (multiple events).
Was/were usually applies to something done in the past that no longer applies (single event).
- The well had been producing clean water.
- The well was producing clean water.
The first sentence implies that the well still is producing water, but it's no longer clean for some reason.
The second sentence implies that the well is no longer producing water.
Of course, context is very important. Here's another example:
- I had been running.
- I was running.
The first sentence implies that 'I' had, at some point of time, run. It could have been earlier in the day, or even the night before.
The second sentence implies that 'I' have just finished running a little while ago.
As you can see, context is heavily implicated. How long is a while?
- I had been running to get fit.
- I was running to get fit.
The two now emphasize two different things. The first implies that perhaps 'I' originally ran for health benefits, but continue to do so for other reasons. The second implies that at one point they ran to get healthier, but a strong implication that they have stopped.