I am seeing this in my current 1.5 game.  A powerful ship I recently designed so I can use it to take over the galaxy is no longer available.  I thought it was because I ran out of resources, then I realized I wasn't using any special resources for it.  It was just gone.  I do have two ships I designed that use Antimatter that show in the shipyard list that I can't build because I am out of Antimatter, so the missing ship is not missing due to a lack of resources.  Again, it is just gone.  I hope it will show up again after enough turns so that I can continue my conquest.

Good question.  I had no idea, so I checked.

I loaded an earlier save, went to the ship designer and found I could build a medium ship with a total of 82 mass.

I loaded my current save, went to the ship designer and found I could build a medium ship with a total of only 78 mass.  I could also see my missing ship in the designer.  Its mass is 82/78, so it is too big to build currently.

Thanks for clearing that up.

You are right, it was Helios Ore.  I went and traded for a couple and my missing designs came back.