...EDIT:: Let me state the events more clearly...
Loaded saved game, did not take a turn, just clicked on shipyardMade a new ship design without components, just the shell,
Saved the ship design,
Bought the ship, completed one turn so that I could see how it looked out in the "open"
Quit the game (Did not save the game, before exiting.)
::At a later date::
Loaded said game,
ship design not in menu
Upon investigation found the ship name and files in the proper folders...
Unable to resolve. Hope that helps..
That has always been standard in GCII: DL and DA and I would assume TA, if it wasn't changed.
Changes to the Ship folder do not take effect in an already ongoing game, for some reason.
If you don't save the game after developing a new design, the design itself is saved for future games, but is not considered available for THAT game, even if you have all the req'd techs, because as you didn't save, the computer has no "memory" of this change to the ship folder being made during that game, so thinks the file must have been created elsewhere and ignores.
It works much the same way it would if you were playing two games concurrently, you can't design a ship in one game, save, open up your second separate game and find the ship "in that universe" even if you are using the same ship style and have all the required techs.
However if you start a new game, your ships will pop up as appropriate...or if you start a new Battle of the Gods all of your ship designs will be immediately available. As it seems the computer "resets" your shipyard to "include all" at the beginning of every new game.
So it's a simple as saving the game after you complete your design. Just close the Shipyard window and save. Now the design is "in the game." Now go do whatever you want and restore the save when ready.
All concerned: I've found that the best way to cleanup the Shipyard is to create a "junk ships" folder inside the Ships folder. Since the file names are relatively easy to recognize it's simply a matter of moving the "junk" to the Junk Ships subfolder. Additionally, if you ever decide something wasn't junk after all, move it back and there you go. Takes significantly less time than deleting it through the Shipyard and a lot less permanent.
Of course your changes to the Ships folder in or out will only take effect at the beginning of a new game.