Any military design, so say I had ten escorts, ten frigates, ten destroyers, ten cruisers and ten capital ships. I researched, for example, Shaterforce lasers, and updated all designs to replace the old blasters. At the point in the game I was I had about 30 colonies (with only seven odd spaceports). I ordered each ship to retrofit into the latest version (yes, the new design was shown), and yes, I had enough materials - I had no problems building new ships of those designs.
When I left the "ship screen", all ships had orders to retrofit. Some did, some just seemed to ignore the order.
As I said above, I think I am doing something wrong / not understanding something properly, I just can't figure it out. Anyway, thanks for the continued thoughts :).