I thought that having Duplicate Toolpath Links checked they would bring the toolpaths over the new copies, but when I look at the toolpaths, they only exist on the original.
Unfortunately, there is no way to keep the layers - the copies all go to the current layer.
So, one approach would be to hide all layers except one, make it active, and do a linear array of that. Keep switching through all the layers, so you are only working with things from one layer at a time.
It’s a bit tedious, but not very difficult. The linear array options are ‘sticky’, so once you set them you can just bang them out.