In this scenario, the user selects a whole assembly (including subassemblies, parts, .etc) by mouse (fence select), and does a copy/paste into a new assembly. Consequently, the assembly structure of the new (inserted) assembly is broken, and there no subassemblies.
SolutionThis is working as designed.
A user cannot select assemblies directly with the mouse, e.g. by fence select. Since an assembly itself contain no bodies, any selection done this way, will only select the bodies of the included parts. So all PARTS will be selected, WITHOUT any assembly structure.
Subsequently, only the parts will be pasted, not the assembly structure. Therefore, any relationships will be broken, and so the positions of the parts will effectively be just hanging in space.
Best practice is to select from the PathFinder as this will allow assemblies to also be selected and copied. After pasting, the assembly structure will be maintained.
There is also a very quick way to copy the whole assembly into a new file.
1) When opened, do an "Assembly of active model". This will create a new parent assembly, including the whole assembly underneath it.
2) Click on the inserted assembly, then select "Disperse" from the Home - Modify tab. This will transfer the assembly structure to the new parent assembly and remove the original parent assembly.