So do you make the save file by running the level one time, activating the trigger, go to another level, then go back to the level you want and save at the very start.
The game automatically MAKES a save at the very start, you don't have to, just backup the autosave.
Also, remember that in the real run you'd have to do this when doing multiple passes of a level ANYWAY just so that enemies are in the right positions / you can't pick up the same items twice.