Con el siguiente código he logrado solventar mi problema.
Código [Seleccionar]
@echo off
set count=0
set ren=-1
for %%x in ("%~d0%~p0\register\data\*.jpg") do (
set /a count+=1
)
setlocal
for %%i in ("%~d0%~p0\register\data\*.jpg") do (
set /a count-=1 & set /a ren+=1
) & call :ren
endlocal
echo En total hay %count% archivos
pause > nul
exit
:ren
echo count=%count% , ren=%ren%
pause > nul
set rename=r%ren%
ren "%~d0%~p0\register\data\%count%.jpg" "%rename%.jpg"
goto :eof