I had a problem on updating some sites and found the solution, so wanted to post incase anyone else has the same issue. I had a few sites with sliders that, on updating to 3.5, the sliders disapperaed from the site, howver all slides etc stayed in tact in cp. These sliders were using short codes and the slides were allocated to a category. In 3.5 check the short codes for a cats parameter and set to the category name of the slides. That fixed.