I've just opened Birth of a Legend.
has-arrived-delay 1 "Fractal"
ship-guardian-threshold
rand 6 17
"Fractal 4"
That's where I think the problem is... I never use so low values, I set something like 15 - 30/35. Sometimes FS may be not that fast to "catch" a fighter in time and protect it(that's the impression I have...it may be false). If that Scar is going to appear again, you should leave it with >20% of hull integrity 
EDIT: Reasonable values needed...
Bear in mind that I'm not approaching the problem as a FREDder trying to hack his way around the problem. I'm looking at it as a coder trying to fix the code so that no stupid hacks are needed.
The problem is nothing to do with the game "catching" it in time. That might be an issue if you were trying to activate a ship-invulnerable when the ship reached a low number of hitpoints as it's quite possible that the game could run through all the ship kill code for that frame and only later find a SEXP that was supposed to trigger and save that ship.
This should not be an issue with ship-guardian-threshold. The SEXP is meant to work in a different way, setting a variable that is checked every time the game goes through the ship_do_damage() function and not allowing any damage to be done which would push the ship below it's threshold value.
If Ship-guardian-threshold worked the way you thought it did there wouldn't be much point in having made the SEXP in the first place. It would be exactly the same as
when
->
--hits-left
--alpha 1
--threshold value
-ship-invulnerable
--alpha 1
Replay mission...nuff said..
You can't fix EVERYTHING...nor should you try...
The fact that something is difficult to do is no excuse for sloppy game design. If you're willing to put out a mission full of bugs then that's your own option but I'm certainly not putting out a bug riddled campaign just because I can't be arsed to spend some effort fixing problems.
Having a main character killed in a mission and then resurrect in the following one is abysmal game design.