The past perfect continuous tense is used to talk about an ongoing action that started in the past, continued for a period of time, and was still in progress at a specific point in the past. When forming questions in the past perfect continuous tense, we use the auxiliary verb “had” followed by “been” and the present participle form of the main verb (-ing form).
Here’s the general structure for forming past perfect continuous questions:
Had + subject + been + present participle?
Looking in corpora, we see that this structure is very rare. Here is 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?