I use folders in my projects and I add files by links. The recent versions of Studio work but the solution explorer view is goofy.
I saw it become goofy while I watched.
I had a good project. Then I added the usb_user.cpp file by link in the USB_WinUSB folder (near the bottom). It looked okay but the project wouldn't build. It said it couldn't find the .d and .o files for the .cpp I just added. I looked in the folder in Debug, and it was true. the .d and .o for the other .cpp files was there, but not for the file I just added. I could compile it by right clicking and hitting Compile, but it still couldn't build,
Then I killed Studio and restarted it. Now it built, but it had created 2 new folders to put the new .cpp file in. Another "Steve_atmel" and USB_WinUSB. It looks goofy. I see there is aother "System" folder there too, but Studio apparently created that earlier.