I asked Chondrite about the issue with the AI only assigning 1 Dockyard to the re-added Heavy ships. This is what he said:

The AI in this game has exact specifications scripted for every type of ship or tank or template it wants to build. Anything that it doesn't identify as being close enough to whatever it actually wants to build (it doesn't want to build just any old carrier design, it knows exactly what modules etc. it wants), it simply drops from its queues or production. With some exceptions possibly, such as a ship construction with a certain amount of progress.

This is probably the reason, but there could be other reasons such as the ratio of certain ship types it wants in its fleets.

So if someone wanted to fix this, they would have to create AI ship design scripts that match these ships. Otherwise it won't assign more factories to them.