AHA, so that's what happened! I was unsure why that bit had changed and just wanted to make you aware 
Thank you for the lesson in best practice. I'm not one who's usually very active on forums but will endeavor to be better haha.
Ok so I am including some example files so you can hopefully get a better idea of what I'm asking.
In the source file there is an RGB layer, In the channels there is a Alpha 1 layer, And in PATHS there is a clipping Path.
So the main purpose of the script was to ensure the 'destination' files have the Clipping path. Which is why we are copying over the RGB layer from the Tif to the PSD.
However as these were output as TIF the layer has been flattened to not include transparent pixels (white background). (limitation of the process we are using unfortunately and no way around it)
I'm hoping once we have copied the RGB layer over we can then use that Alpha Channel to delete that White background in the main layer or apply it as a mask?
As I couldn't find a solution for using the Alpha Channel I instead created a 3rd folder 'MASKS' Hoping I could use that as a way to apply the Mask.
Again no luck (I'm a noob scripter)
So I'm asking if you know a way to achieve the above in either of the ways outlined.
Using that Alpha Channel or a seperate file.
Thank you for baring with me. Your help has been extremely appreciated!
Regards Jimbo
