I am changing laptops and going to windows 8.1 and so need to 'carry' my emails on to the new machine.

I have exported my emails a folder on my desktop (it took a long time) and then tried to copy that to a pen drive. Lots of files would not copy. Therefore, I have tried to export the emails direct to a folder on the pen drive. This happens in about 1 second and tells me it has exported them. However apart from some folders and odd files there are no emails on the pen drive. Is there some flag that prevents a second copy? If so, how can I over com it?