With the recent Japanese restoration of the Sistine Chapel Ceiling, Michelangelo's mastery of colour and sculptural illusionary mass has come to be seen in a whole new light. Many art connoisseurs were "shocked" at the vibrant depth in the magnificent colour found beneath the centuries of candle soot and grease.
When I was in college, I had an art history professor who had been fortunate enough, while a student in Rome, to have viewed the Sistine frescos from as close as 10 feet (rather than 78 feet from the floor below). He swore some of the cracks in the ceiling had been painted in, presumably by the master himself. Of course such an observation is doubtful, given the short time span during which Michelangelo worked on the ceiling. Likewise one would have to wonder as well, why he would go to such lengths.
There was no word as to whether or not the Japanese actually found any evidence of such a deception but presumably they would have "restored" them away if they had.