I just played through the first mission of the Dark Avatar campaign. I saved towards the end of the mission, turned off the computer, and came back to it later. When I loaded up the quicksave, I noticed that the custom ships I had designed (even though I had used preloaded templates since I was in a hurry to get through the mission) were gone! They still existed in the game, but there is no image for them on the ship builder (icon on left and in main view), on the game screen, or in the icons representing the ships. Luckily I usually play zoomed out to tactical view and all the invisible ships were visible there. The ships that I had not modified (the one's I started the game with and the "standard" ships in the ship builder) were still visible. As were the templates I had built my custom ships off of. What's more, the Drath's ships now all looked like Dread Lord organic hulls (no extras).
Anyway, I quickly finished the mission and went on to the next mission (without quitting DA). All my custom ships were visible again! The constructor and colony ships that I had made in the last mission and that had become invisible were now totally normal. I have yet to load up that game, so I don't know if the bug will repeat itself, but I don't have time to load it tonight.