There seems to be an issue with mass importing where if there is a folder structure it will refuse to save thing. So far I have only noticed the issue with textures but it is time consuming to import all the texture folders individually.
Not 100% sure but I think importing Fbx with a folder structure ignores the model textures aswell.
Hi Handsome_Jack,
Thank you for your request. I have entered a feature request, UE-12179 to be considered by the development staff.