Код:

@Echo Off
Set "WhereF=D:\Файлы"
Set "WhereD=D:\Папки"
FOR /F "usebackq tokens=1,* delims= " %%i IN (`Dir "%WhereF%\* *.pdf" /B /A:-D`) DO (
FOR /D %%d IN ("%WhereD%\%%i *") DO (
If Exist "%WhereF%\%%i *%%~xj" Move /Y "%WhereF%\%%i *%%~xj" "%%d\"
)
)