I suspect this is a limitation of the beta.   The autodesigner is updating the ships with the new technology...  as the new ship is not the same as the obsolete one it shows up.

For now we just deal with it, but i'm hoping this is corrected so once a design is "obsolete" it no longer gets improved.

There is a difference between ship designs and ship blueprints.

When you design your own ships, you are making designs. These designs are very precise, such as 5 harpoon missiles, 2 ion drives, 3 life support, 1 sensor, etc. They do not update unless you update them by making a new design. Obsoleting those designs is also your job. It is a very hands on, manual way of doing things.

A ship blueprint however, takes a more meta view of what it means to be a certain kind of ship. It will include details like insert beam weapon here, but it will otherwise be something that could be swapped out for a better version later. I'm actually studying how to mod them right now. There are entries for required components, a list of components (which I'm guessing is added in using the given order they are listed in if the ship has room), and filler components (which I'm guessing it is what will be used to repeatedly fill the ship with if there is still any room left over).

You pointed me to that link a few days ago in a different thread. I finished reading it before writing my above post. Thanks for the link though. I plan to make use of it soon.