In single missions, its impossible for a ship to show up in visual range (or possibly at all) after a mission starts. This includes spawning using the "Events" options or scheduling any ships to appear after the mission start. There has been some speculation/debate whether this is a bug or a feature to prevent "phanton ships" from appearing out of nowhere. I too have had problems with deleting ships in single missions. I think its bugged.
Trust me, its going to be impossible to do exactly what you want. Sorry
I've been there too.
