You would have to be "editing in place" the cylinder assembly to drag the rod. In a higher assembly the cylinder assembly is considered one component. You could make it (the cylinder assy) an adjustable assembly and assign a variable for the rod extension. That way the rod could have different extensions in different assemblies.
So I will not be able to move it freely in the main-assembly?
I need to split it up and import all the parts into the main-assembly, to make it move like it did originaly? Seems odd.