Well, I have not
It was my understanding that all settlers have the "Protected" flag. If that is the case, it should be impossible for them to be killed by other NPCs unless their deaths are scripted. Protected actors can be killed by the player character at any time, and apparently turrets, mines, or explosions caused by the player character (meaning turrets or mines that you place, explosions that result from a shot you fired, etc.) count as damage from the player character.
I have observed settlers exhibiting the characteristic "bleed out" mode animations when they are engaged in combat with hostile NPCs, so I am pretty confident that settlers do have the Protected flag at least some of the time. Not all settlers of course, but the ones that are residents of your allied settlements.
There are a number of possibilities for the discrepancies in our observations.
1. One of us is just plain wrong in what we have observed.
2. Settlers protected status is changed to normal while the player character is not in the cell
3. Else (and this would achieve the same effect) the scripted damage effects of failed "help settlement . . ." quests simply mark a settler or two or three as dead depending on the values being used in the script.
4. The deaths of settlers you are observing were caused by turrets, or other stationary actors (mines, tesla fields, etc.), which were placed there by the player character; as I said, it appears that these are equivalent to the player character in terms of causing lethal damage against protected actors.