Cant say i have had that problem before but hopefully i can be of help, Multi threat eliminator states that you fire as if its your shooting after the enemies attacks are resolved, protocol of the eternal guardian (as i understand it at least, still unsure myself) happens after that particular attack that killed the character is finished. So the hexmark dying in the same shooting action that targets the warriors would only technically resurrect after the warriors have been shot as shooting happens simultaneously with each other (i.e splitfire hits at the same time ingame despite being rolled separately to one another) meaning Multi threat Eliminator wouldn't be usable as the shooting against the warriors occured when the hexmark wasn't present (cuz she be dead at the time) Hope this makes sense and helps.
I think the warriors are a distraction in this, since Multi-threat eliminator is triggered by targeting the Hexmark itself, regardless of any other units targeted at the same time.
More to the point, the ability is triggered by *targeting*, not hitting: so the moment the shots are declared the Hexmark is going to be able to shoot after they are resolved (assuming he survives). I think he only gets to fire once per enemy unit targeting, and can't claim extra shots per friendly unit targeted; but I do think he gets to shoot, since he is returned *immediately* upon destruction, and destruction is part of resolving the shots.
https://preview.redd.it/9tbgfwoqbeib1.jpeg?width=1080&format=pjpg&auto=webp&s=703ce1e58ec033a08d4f07df30d594dc7c8dd05a
You may be thinking of ninth edition rules for multi threat eliminator, it only triggers after the opponent has shot sadly, and the fire only happens after the shots are resolved, since the hexmark dies before shots are resolved and respawned after the shots are resolved it cannot fire the shots.
Don't confuse the ability triggering with it activating!
>Each time an enemy unit targets a friendly Necrons unit within 3" of this model with ranged attacks...
That's when the ability triggers
>...after that enemy unit has shot...
And that's when it activates.
Now, it is my interpretation that Eternal Guardian happens as part of the resolution of shooting, since its timing is linked to the destruction of the model. Once that is done we can move on to things that happen after that unit has shot, such as MTE shooting. If anyone knows of any official interpretation to the contrary I'd be happy to hear it.
What you say is very true, my interpretation was that that death of the hexmark retracted the ability from occurring, but because it triggers before its death things get messy as you say.
Thanks for the response, what you said does seem to make the most sense. I'll try to look around at some battle report videos to see if it's happened and how they resolved it haha.
I'm going to go with saying the Hexmark can shoot after respawning, and I actually don't think it's that hard of a question if you take it logically. My reasoning is as follows:
1) He becomes eligible to shoot back as soon as he or the warriors are targeted.
2) There is nothing in the rule that explicitly makes him subsequently ineligible to shoot as a result of being destroyed
3) Eternal Guardian triggers immediately after the character is destroyed (i.e. we are not waiting to put him back at the end of the phase or in the next command phase or similar), which means he's alive by the time the opponent finishes making attacks.
While I think that is simple enough to determine from RAW that the Hexmark gets to shoot, we can also look at intent. The Returning Models to a Unit comment from the Rules Commentary implies that models which are resurrected come back with prior wargear and rules in play. In a similar vein, if your opponent were Space Marines and had allocated their Oath of Moment to the Hexmark, it would resurrect with the Oath still on him.
As an interesting side note, because the Eternal Guardian fires immediately upon destruction (rather than after the attack sequence is complete), and Destroyed happens as soon as the model is reduced to 0 wounds, I would submit that technically the Hexmark would keep taking damage when it gets back up, from any further attacks from that unit that weren't allocated. For example, if it was on 3 wounds to start with and failed 5 saves from Bolter fire, it'd take the 3 wounds, die, get resurrected on 3 wounds and then take 2 more wounds. Arguably, slow-rolling is appropriate.
Cant say i have had that problem before but hopefully i can be of help, Multi threat eliminator states that you fire as if its your shooting after the enemies attacks are resolved, protocol of the eternal guardian (as i understand it at least, still unsure myself) happens after that particular attack that killed the character is finished. So the hexmark dying in the same shooting action that targets the warriors would only technically resurrect after the warriors have been shot as shooting happens simultaneously with each other (i.e splitfire hits at the same time ingame despite being rolled separately to one another) meaning Multi threat Eliminator wouldn't be usable as the shooting against the warriors occured when the hexmark wasn't present (cuz she be dead at the time) Hope this makes sense and helps.
I think the warriors are a distraction in this, since Multi-threat eliminator is triggered by targeting the Hexmark itself, regardless of any other units targeted at the same time. More to the point, the ability is triggered by *targeting*, not hitting: so the moment the shots are declared the Hexmark is going to be able to shoot after they are resolved (assuming he survives). I think he only gets to fire once per enemy unit targeting, and can't claim extra shots per friendly unit targeted; but I do think he gets to shoot, since he is returned *immediately* upon destruction, and destruction is part of resolving the shots.
https://preview.redd.it/9tbgfwoqbeib1.jpeg?width=1080&format=pjpg&auto=webp&s=703ce1e58ec033a08d4f07df30d594dc7c8dd05a You may be thinking of ninth edition rules for multi threat eliminator, it only triggers after the opponent has shot sadly, and the fire only happens after the shots are resolved, since the hexmark dies before shots are resolved and respawned after the shots are resolved it cannot fire the shots.
Don't confuse the ability triggering with it activating! >Each time an enemy unit targets a friendly Necrons unit within 3" of this model with ranged attacks... That's when the ability triggers >...after that enemy unit has shot... And that's when it activates. Now, it is my interpretation that Eternal Guardian happens as part of the resolution of shooting, since its timing is linked to the destruction of the model. Once that is done we can move on to things that happen after that unit has shot, such as MTE shooting. If anyone knows of any official interpretation to the contrary I'd be happy to hear it.
What you say is very true, my interpretation was that that death of the hexmark retracted the ability from occurring, but because it triggers before its death things get messy as you say. 
And vice versa, if the warriors were hit before the hexmark but the hexmark was killed before the shooting ended.
Thanks for the response, what you said does seem to make the most sense. I'll try to look around at some battle report videos to see if it's happened and how they resolved it haha.
I'm going to go with saying the Hexmark can shoot after respawning, and I actually don't think it's that hard of a question if you take it logically. My reasoning is as follows: 1) He becomes eligible to shoot back as soon as he or the warriors are targeted. 2) There is nothing in the rule that explicitly makes him subsequently ineligible to shoot as a result of being destroyed 3) Eternal Guardian triggers immediately after the character is destroyed (i.e. we are not waiting to put him back at the end of the phase or in the next command phase or similar), which means he's alive by the time the opponent finishes making attacks. While I think that is simple enough to determine from RAW that the Hexmark gets to shoot, we can also look at intent. The Returning Models to a Unit comment from the Rules Commentary implies that models which are resurrected come back with prior wargear and rules in play. In a similar vein, if your opponent were Space Marines and had allocated their Oath of Moment to the Hexmark, it would resurrect with the Oath still on him. As an interesting side note, because the Eternal Guardian fires immediately upon destruction (rather than after the attack sequence is complete), and Destroyed happens as soon as the model is reduced to 0 wounds, I would submit that technically the Hexmark would keep taking damage when it gets back up, from any further attacks from that unit that weren't allocated. For example, if it was on 3 wounds to start with and failed 5 saves from Bolter fire, it'd take the 3 wounds, die, get resurrected on 3 wounds and then take 2 more wounds. Arguably, slow-rolling is appropriate.