追加ツール不要
先頭のゼロ付与なし、重複チェック無し

set rnmcounter=1
for /f "delims=*" %%i in (filelist.txt) do (
setlocal enabledelayedexpansion
ren "%%i" !rnmcounter!%%~xi
endlocal
set /a rnmcounter+=1
)