I was searching for costume ideas for a doll for the Treasures of the Gypsy Challenge when I came across a portrait of a Young Woman With Unicorn, attributed to Raphael. Further, research, however, revealed that this was not the original painting.
For a long time the painting was identified as a painting of Saint Catherine of Alexandria by Perugino. The painting at that time showed a young lady holding a Catherine Wheel. No unicorn.
In 1934 to 1946 massive overpainting was removed to show the familiar version and the painting was now attributed to Raphael.
In 1959 an x-ray of the painting showed that there was originally a lapdog where the unicorn now sits. Now some people think that Raphael only painted the background and who knows who added the unicorn and who later painted over the unicorn and added the Saint Catherine details.
Art history seems to be full of these "painting overs" such as the disappearance of the three angels in Lorenzo Lotto's Madonna delle Grazie.
Other mysteries are the interpretations of the painting commonly known as The Arnolfini Portrait. You must draw your own conclusions.