Lucy's journal is the key to the plot
My theory is that at some point in time Garcia Flynn found/stole/acquired Lucy's journal proving time travel exists. This led to Flynn coming up with the plan to steal the time machine in the first place.
Flynn is now carrying out acts already mentioned in the journal. Basically he is fufilling history.
The Hindenburg incident did not butterfly away Lucy's sister. I think Flynn changed something else and now Lucy is trying to track down that event.