I am having this issue when importing geometry after installing 2016 on new machine as a fresh install. This happens on all imported geometry (STEP, X_T, etc.)
After import as an assembly, the model looks great. I SAVE ALL the entire assembly as is - no change. I close the assembly. After opening the saved assembly it no longer can find any of the parts that were suppose to have saved during the SAVE ALL.
The only way around this is that after importing i have to open ALL the part files individually! this is ridiculous as some geometry has hundreds of parts in the assemblies.
I also notice if i go into advanced save, it lists all the part file and subassembly locations as FILE NOT FOUND after importing the file. But i don't understand why after import, it doesn't load these files. These models are shown in the model space and i can select them. It just won't save them unless i manually open them. I never have had this problem before this fresh install. Any help would be appreciated.