Hey Joe. Have a good time on Mother's Day.
I am impressed on what you did in the mission, "Shackles of War," rescuing the Damocles. You did it in your second try. Believe me, my success chance in that mission is only 15%. Even I have difficulties to beat my own creation.
In many missions, you will find the "self-destructed" thing. I use that for "scripted" events. Meaning that ship will inevitably be destroyed, demanded by the story. In many cases, I use the self-destruct thing to destroy an invisible, invulnerable ship or ships. These are scenario "markers" since in my mission designs, many things can happen, many branching scenarios. The FRED's equivalent, the "Event true" SEXP is not that robust and limited in scope so I use this. You will find a ship in the mission Event list (F4) that is named "Mission Objective." That's actually a ship, it does not move, no weapons, friendlies and hostiles can't and won't target it, invisible and invulnerable because it's only an event marker. It will self-destruct when a certain scenario or event happened.
But in case of the mission to destroy a Shivan convoy, Capella self-destructed, I was surprised. It's a bug. Capella should have jumped out. I'll check into it and fix it.