Trivia: Victoria Tennant hated the scene where her character was to be killed off so much that she refused to film it and walked off the set. The scene then had to be done by a stunt double.
Trivia: Flowers in the Attic author V.C. Andrews has a cameo appearance in the film as a window-washing maid.
Trivia: Victoria Tennant plays Jeb Stuart Adams' mother in the film, even though in real life she's only 11 years his senior.
Answer: Short answer, possibly, but we'll never know to what extent if it was. The film is based on the novel written by Virginia Andrews (V.C. Andrews) in 1979. In her pitch to publishers, she said it was not truly fiction. Her claim is the story is based on the life story of a doctor she met when she was younger. The name of the doctor was never revealed. She also wrote sequels to the original book which would have most likely been complete fiction, and there was a prequel ghost-written that most certainly wouldn't have been based on true events.
Bishop73
Supposedly, the doctor told her that he and his siblings were locked in an attic for six years to preserve family wealth. This is according to "an unidentified relative" of VC Andrews. Source: Wikipedia. As you say, we will never know how much was true.