Having positioned scouts so that I would be able to see everyone who hangs out in my space, I then decided to upgrade the existing design, which I did. Then I obsoleted the old design. I don't know why I hit Yes to the dialogue that followed, but I must have done because when I was finally finished with redesigning new ships, and got out to the main map, all I could see is what my non-scouts, starbases, and planets could see. Which isn't a lot.
I think there should be some kind of anti-stupidity measure so that you don't accidentally decommission a whole bunch of ships which are vital to your empire's operation