When i select a ship and choose upgrade in the shipyard, change the components and then save under a different name all planets that were building the original now have empty queue.

That seems to be ok but when going to the governor and selecting the nothing building queue these planets do not show as doing nothing so for the governor they are still building but none of the ships in the list are showing so it must be the old design that was renamed.

You have to go to each planet and change the queue manually to fix this