Ответ:

1. We had got the expert evidence by the end of the working day.

?   Had we got the expert evidence by the end of the working day?

-    We hadn't got the expert evidence by the end of the working day.

2. Pretrial examination had been over by the end of last week.

?   Had pretrial examination been over by the end of last week?

-   Pretrial examination hadn't been over by the end of last week.

3. After they had finished analyzing the handwriting, we came to an important conclusion.

?   Had they came to an important conclusion, after they had finished analyzing the handwriting?

-   They hadn't came to an important conclusion, after they had finished analyzing the handwriting

4. They had found the escaped prisoner before the sunset.

?   Had they found the escaped prisoner before the sunset?

-   They hadn't found the escaped prisoner before the sunset.

5. I had known the witness for a long time before she committed the crime.

?   Had I known the witness for a long time before she committed the crime?

-   I hadn't known the witness for a long time before she committed the crime.

6. They had passed 3 property laws before going on holiday.

?   Had they passed 3 property laws before going on holiday?

-    They hadn't passed 3 property laws before going on holiday.