For what it's worth, when I was putting up my comsat network I would often forget to rename sats after getting them in orbit. So I would have multiple sats with the same name. Had to go to space center, focus them, and rename them. Very annoying. Each sat was launched individually in it's own launch vehicle, then released. After release the default name was something like <saved name from VAB> Probe. Haven't gotten the bugged space center except when I had too many addons loading. Used reduced res textures and fixed that problem. Never had any crashes or duplicated craft yet.