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Попробуй так:

Код:

@echo of
setlocal enabledelayedexpansion

set "MainDir=%~dp0Base"
set "OutDir=%~dp0KONTYNER"

for /f "tokens=*" %%a in ('dir /a-d/s/b "%MainDir%\*.txt"') do (
   set "TxtDirPath=%%~dpa"
   set "OutSubDir=%OutDir%\!TxtDirPath:%MainDir%\=!"
   if not exist "!OutSubDir!" (
      md "!OutSubDir!" && move "!TxtDirPath!*.*" "!OutSubDir!" && rd "!TxtDirPath!"
   ) 
)