In the shipyard, I deleted one of my user made ships. However, in the build ship shortcut in the window when you select a planet, it still shows up in the list. And there's multiple copies of them. In the research tech tree, under some of the research options, it will still show what is need to unlock that ship. There are also multiple copies of the same thing with different number of other techs required.
What I did that might cause this bug is that I upgraded one of my ships and saved it under the same name. I already have a few of them on the map when I did this. So when I clicked done, it prompted whether i want to upgrade them and I clicked yes. I did this a couple of times. Anyway where I can remove them permantly manually? i.e finding the folder where its stored and delete the entry?