I don't see what there is to "fix" here.
The base templates cannot be deleted as the game automatically updates those. so you have a ship that is a base name like the Torian Lobster.
You edit the Torian Lobster and rename "Green Killer"
you then upgrade a technology. The game does not modify custom designs. so you now have Lobster L (Upgraded Lobster), and "Green Killer" (Not upgraded)
This is not broken. changing this behavior would break the game.
Now what I would like to see is the ability to Obsolete or hide design and have the design not show back up after it has been upgraded with new technology.
it would also be nice if once we went in and made Green Killer Mrk1 the game would realize that this is an upgrade over Green killer