Код:
@Echo Off
Set FDir=D:\Delete1
Set SDir=D:\Delete2
FOR /F "usebackq delims=" %%d IN (`Dir %FDir% /b /A:D`) DO Call :Select "%%d"
GoTo :Eof
:Select
FOR /F "usebackq delims=" %%f IN (`Dir "%FDir%\%~1" /O:-D /b /A:-D`) DO (
Md "%SDir%\%~1" >nul 1>nul 2>nul
Copy "%FDir%\%~1\%%f" "%SDir%\%~1\" >nul
GoTo :Eof
)