Oh, I see. That is awkward.

Also ships with the same name are hidden. For example with the Phidi, having annexed the Orthin, I only get the Phidi "Military Transport" in the list. To get the Orthin variant appear, I had to go to the blueprint editor, create a new design, there the Orthin hull is available, and give it a different name (I used "Assault Transport"). Orthin ships are a lot better, they have system slots for shields.