I don't think there is anything out of the box in SW that will do what you are currently doing. I would post this in the API section and see if someone may be willing to modify you existing scripts to ready the SW file references. then you could stay with your existing process, just updated to your new tool.
one warning though, moving files can cause issues where the assembly/drawing can't find its parts/assemblys - but it sounds more like you are achiving the files rather than expecting to use them - so it may not matter in your case.
Thanks for the info, I will past this in the API Section and see if there is some help there. I thought moving files here would be easier than in NX, guess I just have more seat time (and programming time)...