Discrepancy in folder contents display under Studio Project and Windows explorer

Hi experts,

I need to translate files under Studio 2015, SR2 project.

The customer file structure under Windows Explorer e.g. looks something like:

Folder x

           Sub-folder X1

                   file X1-1

          Sub-folder X2

          file 1

          file 2

Folder Y

        Sub-folder Y1

                file 1

                file 2

When I create a project with folders X and folder Y, the folder/file view under Studio project e.g. looks something like:

Folder A                                               (Folder A shown here which was not visible under Windows Explorer)

           Sub-folder A1                          (Sub-folder A1 shown here which was not visible under Windows Explorer)

                     file A1-1                          (file A1-1 shown here which was not visible under Windows explorer)

          Sub-folder A2                          (Sub-folder shown here which was not visible under Windows Explorer)

                     file A2-1                         (file A2-1 shown here which was not visible under Windows explorer)

Folder X

           Sub-folder X1

                     file X1-1

           ---                                              (Sub-folder X2 not shown here which was visible under Windows Explorer)

           file 1

           file 2

Folder Y

        Sub-folder Y1

                     ---                                             (file 1 of Sub-folder Y1 not shown here which was visible under Windows Explorer)

       file 2

My task is to translate  files in folders which are visible under windows Explorer.

Though strange, but so far as the display of "additional folders/files" and files under Studio project is concerned, I am basically not worried - because I don't need to translate these anyway..

But if folders and files which are visible under Windows Explorer but are not displayed under Studio project - it becomes a serious issue.

I think, this might be a problem with customer folder(file structure, but I am not sure where to start and what to look for ?

Customer claims that the folders/files have not been extracted from a server base project.

On my side, I have created a project with default settings, 1TM. 1TB and all language pairs (have also tried with a single language pair). 

So how to set-up a project where all files visible under Windows Explorer are also available for translation under Studio project?

Any tips or suggestions would be most welcome.

Thanks and best regards

Shyam