I am running test version 1.05.351507.  A game save that should allow you to see this issue is available here:

https://www.dropbox.com/s/tfr0z2z285k9kn8/ShipyardBugDemo.GC4Sav?dl=0

I have run across a bug in the ship designer.  I have seen it a few times in different games primarily with huge ships.  The bug is that, when you try to modify an existing ship design, the current components of the current ship design appear on the graphic appearance of the ship, but do not show-up in the list of component icons at the bottom of the screen.

You can see this by following these steps:

1. Start the game and load the saved game whose link appears above
2. Double-click on any Gemini shipyard (the Gemini are my custom civilization)
3. Click on the "New Design" button in the bottom right-hand corner of the screen
4. Scroll down the list of Available Designs until you get to the one named "Huge Beast"
5. Click on the one named "Huge Beast" then look at the ship's picture and the icons depicting the components
   1. the picture accurately shows all of the components that I added
   2. the list of icons is missing almost all of the added components

The first screen snapshot below shows what it looks like on my computer.  Note that the only component icon that appears at the bottom of the screen is for the Interstellar Drive component.

1. Next, click on the "+" icon at the bottom left-hand part of the screen to edit the "Huge Beast" ship.
2. The designer does not seem to know about existing component other than the Interstellar Drive even though the Design Details section on the right-hand side of the screen knows about all of the components.

The following steps will make the behavior become even more interesting:

1. Hit the "Cancel" button and confirm that you want to exit the ship designer.
2. Scroll back down to the "Huge Beast" ship which should still be selected
3. Click on "Rock Carrier M4" which should be right below "Huge Beast"
4. Click back on the "Huge Beast" ship and now you should see more icons representing the components of the "Huge Beast" ship, but still not all of them.

The second screen snapshot below shows what this looks like on my computer.  Note that there are now 7 component icons, which is more, but still not all of the components that are in this design.

I do not know if this is a bug in the software or a problem with however you are storing and retrieving ship designs but, whatever is causing this problem, it needs to be identified and fixed.