According to Martin Hewing's Advanced English Grammar:
The difference between past continuous and past perfect continuous is as follows:
When we met Simon and Pat, they had been riding.(=we met after they had finished)
When we met Simon and Pat, they were riding.(=we met while they were riding)
If we keep in mind this difference, will native speakers consider sentences like:"Jane had been suffering from flu when she was interviewed," to mean that Jane had recovered before the interview?