Stephanie,
Yes, It is very unfortunate that his every stroke couldn't be preserved in time. There have been about six major restorations throughout its history. Before the 20th century, there was no science to prove the method in which Da Vinci painted The Last Supper, so artists were sort of ruining it by intervening with materials that were inadequate for such a monumental task. In 1903, it was discovered to be painted in tempera and for the next few years, with the help of photography to identify foreign glue, sludge, dirt, etc. . . cleaned up the surface. More meticulous cleaning was done for the next 20 years. After that, the most recent restoration, in 1999, was meant to finally stabilize it. It is kept in a climate-controlled area.They used fantastic technology and Leonardo's old sketches to help determine the look and colors of the original paintings. Although much controversy has sparked up about the changes and efforts of the people involved in the restoration, I believe that it is the final one.