This is from the Nineties:
"Olivier, Olivier" (1992)
A 9-year-old boy disappears without a trace. Six years later, he appears in Paris, but there are doubts about his real identity.
From IMDb forum:
I saw this film a while ago, and I never understood why the sister slept with the kid they all thought was her brother.
From IMDb forum 2:
I don't think he was literally her brother. I think that when she did that sort of spell thing with the eggs she caused some sort of transmigration of souls that caused the runaway to have aspects of Olivier's personality. So she perhaps knew on some level that he wasn't her brother.