@echo off
if exist ctmp.ini del ctmp.ini
for /f "tokens=*" %%a in (config.ini) do (
if /I %%a==update=yes (
call 2.bat
echo update=no>>ctmp.ini
) else (
echo %%a>>ctmp.ini
)
)
del config.ini
ren ctmp.ini config.ini

------解决方案--------------------
BatchFile code
@echo off
set TmpFile=tmp.ini
set /p ini=<config.ini
if "%ini%" equ "update=yes" (
  call 1.bat
  >"%TmpFile%" echo update=no
  >>"%TmpFile%" echo cop=af
  move /y "%~dp0%TmpFile%" config.ini
)