I think I'm having a similar issue to jayderyu. I made an animation a week or two ago (the same one having issues with replacing sprites that I posted about above). It seemed to be saving just fine, but when I tried to open it today, only one of the sprites was showing up and animating, though all of the keyframes appeared to still be there. The file palette still shows all of the correct pngs, but in the z-order and hierarchy, they are all labelled as object_###, the bones are gone, and when a blank object is clicked the screen goes black or half black, half gray. I tried replacing the blank objects with pngs from the file palette, but none of them have retained their correct positions. They just stack in a pile on the stage and do not animate (though they do get selected instead of showing a black screen). The z-order seems to change still though.
https://dl.dropboxusercontent.com/u/899 ... nshot1.png
https://dl.dropboxusercontent.com/u/899 ... nshot2.png