[megaloman]

Еще вариант без временных фйайлов

Код:

@Echo OFF

Set "cfgIn=Z:\Soft_In\tra la la.cfg"

Set Rep="Dreamcast.Region=333" "Dreamcast.Broadcast=444" "Dreamcast.RTC=5552127595098" "DefaultImage=image.gdi" "Dynarec.Enabled=0"

Set /A N1=10000
Set /A N=%N1%-1
FOR /F "usebackq tokens=*" %%a IN ("%cfgIn%") DO Call :MassTo "%%a"
>"%cfgIn%" (FOR /L %%i IN (%N1%,1,%N%) DO Call :MassFrom "A%%i")

GoTo :Eof                                     

:Rezult
	Set "InStr=%~1"
 	FOR /F "usebackq eol==" %%i IN ('%InStr%') DO Set "Par1=%%i"
	:Begin
 		FOR /F "usebackq eol==" %%j IN ('%~2') DO Set "Par2=%%j"
		If /I "%Par1%"=="%Par2%" Set "InStr=%~2" &GoTo :End                                              
		Shift
		If Not "%~2"=="" GoTo :Begin
	:End
	Echo %InStr%
GoTo :Eof

:MassTo
	Set /A N+=1
	Set "A%N%=%1"
GoTo :Eof

:MassFrom
	Call Set "Arg=%%%~1%%"
	Call :Rezult %Arg% %Rep%
GoTo :Eof

Не уверен, стОит ли обходиться без копии исходного файла