Batch file IF statement fails with "was unexpected at this time"

The shell seems to think that the ) in the third line of your command is the closing parenthesis for the one opened in the first line. You need to quote the arguments containing parenthesis:

@IF EXIST "C:\Program Files\MyAppFolder" (
  icacls "C:\Program Files\MyAppFolder" /inheritance:r
  icacls "C:\Program Files\MyAppFolder" /GRANT "SYSTEM:(CI)(OI)(F)"
  icacls "C:\Program Files\MyAppFolder" /GRANT "Administrators:(CI)(OI)(F)"
)