So I am running SW2011 SP5 x64. The problem I am having is that sporadically SW is removing my subassemblies from my assembly. It happens when I create a new part and then turn that part into a new sub-assembly and try to save the sub assembly externally. It does it if I save the part I created to start my sub-assembly externally or internally to the original assembly. SW saves the parts (both externally and internally) but completely deletes the sub-assembly when I try to save it.