Yes........this is what i am doing. And when i pay and wait a couple of weeks for the upgrade to complete.........it turns into a Battle Axe with generic weapons and no defense.
I think Xtanto was asking about was what kind of ship are you trying to upgrade *to*?
There are two paths to upgrade. One is to have a ship that you designed like your ALPHA FIGHTER and then later on develop some new tech and want to upgrade your old ships.
One way is to create a new ship, let's say ALPHA FIGHTER II for example. Then you select one of your current ALPHA FIGHTER's and press the "upgrade" button. It then take you to an upgrade screen for that specific ship which gives a list of ship to which you can upgrade to. Note you can only upgrade to ships of the same size hull as the current ship (also note that a cargo hull and a Large military hull are the same size and so you can go from a cargo hull ship to a Large military hull ship via upgrade.
When using this method you can also select a check box to upgrade all ships of this class. However the point is that to upgrade in this manner you need to specifically select the ship that you're upgrading to and so if you upgrade to Battle Axe it should be because you specifically selected Battle Axe as the ship to upgrade *to*.
The other way to upgrade ships is to go into the shipyard and select the current ALPHA FIGHTER design and hit the upgrade button there. That will take you ship design screen where you can modify the current design. In this case nothing happens until you "save" the design. If you save the design to the old ship name ALPHA FIGHTER it will say that this is not recommended but it will allow you to do it anyway but will ask you if you want to upgrade all current ALPHA FIGHTER's. If you save it to a new name then it won't ask about upgradin your current ships but if any planets are currently building ALPHA FIGHTER's then those planets will instead start building the new ships.
I think the issue is that folks (myself among them) aren't understanding what it is that you are doing because as far as I know for you to upgrade a ship to a Battle Axe you must have selected Battle Axe as the ship to upgrade *to*.
I think you need to describe your issue in more explicit detail because no one is really understanding precisely what your problem is.