Point 87 in the category of PAST:
past perfect continuous QUESTIONS
A search in COCA:
1 HAD SHE BEEN THINKING ? 23
2 HAD HE BEEN THINKING ? 18
3 HAD SHE BEEN DRINKING ? 8
4 HAD I BEEN THINKING ? 7
5 HAD YOU BEEN DRINKING ? 4
EXAMPLE:
What had she been thinking?