I think there are very few writers alive whose story line didn't change at one time or another. Me??? Well, the end product is nothing like the first draft. For instance:
Illusions of Destiny: Started as a time travel romance where Ianna (the heroine) was an English woman captured by feared Scottish border reiver, Regan (the hero) and spirited off to his run down castle in the wilds of the Scottish Highlands.
Ended up: As a fantasy romance where Ianna was whisked away to a place where mythical animals were every day and the gorgeous hero, Regan, was the sidhe leader. The only scene I kept from one version to the other, was the opening the package scene.
How did this change occur? Don't ask me!
Jewels of the Sun: It started out that Selena (the heroine) was on board a doomed cruise ship that sank. She was rescued by Saxon (the hero) and taken back to Ambrosia, an island that disappeared and reappeared at will. Now, what Selena didn't know was that every ten years, a cruise ship sank and the survivors were taken back to Ambrosia as "fresh blood". In this version, Saxon and his (ex)buddy Kingsley fight over Selena because they both want to marry this piece of "fresh blood".
Ended up: Selena is a treasure hunter looking for the famed island of Ambrosia and the bucket loads of treasure. She's pulled out of the ocean by Kingsley (not the hero) but kidnapped by Saxon (yes, he's the hero). I kept the majority of the story line, I just added a few characters and turned it into an adventure.
In the Shadows of Angels: In this one, Ella (the heroine) was running from her mobster boyfriend because she saw him (and took photos unwittingly) kill his mother. She ends up in Queensland and buys an antique clay angel. What she didn't know (and soon discovered through her dreams) was that a ghost, the incorrigible Lucius Benedict (the hero), came with the angel. When she breaks the angel, she finds a locket and a note stating a curse put upon the poor Lucius. So, she sets off to solve the murder mystery and break Luke's curse by midnight New Years Eve.
Ended up: As a Scottish time travel. Ella inherits a book and is taken back in time. She saves Luke from a beheading and carries on to solve a murder mystery. The only scene I kept from the original version was the buried alive scene. I kept most of the characters but changed their purpose in the book.