make a batch file called changelines.cmd
@echo off
echo.
for /f "tokens=1* delims= " %%a in (%1) do (
if %%a==^<?xml echo. 2>%temp%\newfile.tmp
if %%a==^<scenarioFile echo ^<scenarioFile^> >>%temp%\newfile.tmp
if not %%a==^<?xml if not %%a==^<scenarioFile echo %%a%%b >>%temp%\newfile.tmp
)
copy /y %temp%\newfile.tmp %1
del %temp%\newfile.tmp

now from the command line, do this:
for %a in (*.ext) do changelines %a

replace *.ext with the filename and type of your excel files.