This is something which is pretty easy to replicate. If nobody gets you a save game for this issue, I can start a game for that purpose.
While we are on the topic... Making an upgraded Architect or Supply from the ship design screen gives it an "intrepid" design, which means it does not have the icon of the basic ship. This is specifically an issue, because AI does not design ships with Hyperdrive Plus or Warp, since they have the same speed as their older designs (Hyperdrive or Ion). So it is necessary to create new designs for space-saving purposes. No save game is needed for this .. just look at any save game you've ever gotten (in which the tech for a smaller, but same-speed, engine has been researched). It is an issue.
(edit) for the record, I do, with every ship set, redesign base Ai designed ships to take space-savers (hyperdrive plus, warp) into account. So the AIs do use my designs, and that's all nice and fine. But the AI does not do that on its own. It would be nice if they did.