I would like to leave the project folders the way they were finalized because this provides a reference to what files were used in the assemblies and perhaps is saved in a way that allows you to make changes inside that folder. Again, I am not clear if the Solidworks Assemblies and Parts (Components) need to reside in the same working folder?
You forgot your own question?
Do the parts that make up an assembly need/should be stored in the same folder as the assembly itself?