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How long had they been sleeping-when he woke them up?
The more correct sentence should be "How long had they been slept-when he woke them up?"
because they had ended their sleep after he woke them up.
My question was raised after reading the topic "When to use 'had been' + past participle of the verb"
Correct me if I am being wrong.
Though this question will probably soon be closed as "off topic" or "not constructive", I feel the need to answer it as I hope these simple words of mine can clear OP's doubts regarding this seemingly confusing concept.
In short, past perfect progressive is the correct choice of tense after been.
How long had they been sleeping?
If been is not necessary to be used, you can consider having the verb in past perfect
How long had they slept?
which is slightly different from simple past.
How long did they sleep?
You should not use past perfect after been in this case because it would result in a type of grammatical construction called passive voice.
Not passive:
John had thrown the ball.
A sentence with the same meaning, but passive:
The ball had been thrown by John.
Note: next time when you have a similar question, ask it in ELL exchange. EL&U is not really the right community for it.
