The two sentences I wrote in english roughly translate to
Did you know she was in Berlin? (Asking a genuine question)
You knew she was in Berlin? (And you didn't tell me?!, accusing the other person)
I think Вы знали, что она была в Берлине? is how you would translate the first sentence, but how would you imply the second one?
Did you know she was in Berlin? (Asking a genuine question)
If she was in Berlin before he supposedly knew it (i.e. did he know in 1990 that she was in Berlin in 1975):
Вы знали, что она была в Берлине?
Знали ли вы, что она была в Берлине?
Известно ли было вам, что она была в Берлине? (most formal)
If she was in Berlin at the same time he supposedly knew it (i. e. did he know in 1990 that she was at Berlin in 1990)
Вы знали, что она в Берлине?
Знали ли вы, что она в Берлине?
Известно ли были вам, что она в Берлине? (most formal)
You knew she was in Berlin? (And you didn't tell me?!, accusing the other person)
И вы знали, что она (была) в Берлине?
or, even better:
Она была в Берлине, и вы это знали?
Your second sentence is nonstandard in English, it's colloquial.As for forming sentences containing a reproach or a sort of accusation, we use both affirmative and interrogative sentences supporting them with intonation and words increasing expressiveness(I am not going to consider English sentences была или есть.)
Так Вы знали,что она в Берлине? И не сказали мне? or Как? Вы знали, что она в Берлине?
We can repeat words, pause emphatically
Вы...,Вы знали, что она в Берлине и ничего мне не сказали?
The first question is pronounced with a rising intonation and sounds neutral.
Знали ли Вы,(Вы знали),что она в Берлине?
First things first, tense sequencing. "Did you know she was in Berlin?" is Вы знали, что она в Берлине? No была, which would make it "did you know that she had been to Berlin".
And the most natural and economical way to differentiate between question and accusation would be with intonation alone:
Вы ↗↗знали, что она ↘в Берлине? (question)
Вы знали, что она ↗в Берлине? (accusation)
(The double arrow is a makeshift way to indicate that that pitch rise is greater than the other one and the drop.)
