These are history's best kept secrets.
The Kennedy family was powerful, but they were also cruel. When their eldest daughter, Rosemary, proved intellectually disabled and volatile, they kept it secret for years, and then gave her a botched lobotomy that left her unable to speak.
The Sound of Music is iconic, but it's also a lie. The real Maria von Trapp could be nasty and had an infamously bad temper, but Hollywood turned her into a loving figure to satisfy audiences.
Two of Queen Elizabeth II's cousins were presumed dead until 1987...when they were found in an insane asylum just because they were intellectually disabled. This wasn't even the first time this happened. Just a generation before, the family kept Prince John, who suffered from seizures, completely away from the public eye.
Franklin Delano Roosevelt likely didn't contract polio like most people assume. Instead, it was likely Guillain Barre syndrome. Either way, he kept his now famous paralysis completely secret from the public, even building a tunnel from Grand Central Station to the Astoria so no one would see him in a wheelchair.
The Roanoke colony famously disappeared, with the only trace being the word "Croatoan" carved into wood. It's a mystery for many, but experts believe the colony simply assimilated into the indigenous population.