OK I figured out how to change the flagship after wasting a couple hours looking for complex strings variables and what not I decided to do something really basic and it worked -go figure...
Anyway I change my flagship to a carrier by renaming the entity files for each as well as changing the name on the second line of the file.
Moreover all the players get the new flagship it does not change just for you.
I have not tested that purchase function yet but I will shortly...
UPDATE
The change only affects your Flagship. Once you build a capital ship dock when you click on the battleship or the carrier button that is what is produced.