I've had this happen a few times -- I will create multiple studies, and run just one of them. After defining the stress plot, I will hide parts in order to see certain areas in the assembly. If I leave them hidden and go to run another assembly, the parts are missing from the assembly. They aren't still hidden, they are actually missing. Then, when I try to close the assembly to (hopefully) preserve some of my results, it asks me if I want to save the changes that I've made to the missing components. Has anyone experienced anything like this?