Refit flagships?

Hey, you can refit the flag ship, but you cannot refit commander ships. The commander ships can be upgraded with artifacts, and they benefit from boosting technologies. 

Flagship is medium size hull, so you'd need to create a medium size ship with a survey model, and whatever internal modules of your liking, and then refit the flagship, as you would do with normal ships.

The ship will retain it's level and other bonuses.

Hope this helps

IpityU - Just to clarify what Zabik_2 said.  If the flag ship you want to refit is a commander ship then you cannot touch it other than as he mentioned for commander ships.  Prototype ships (Raptor, Praxis, Retribution, ect.) are also treated like commander ships, so none of those that are flag ships qualify for refit either.

That sucks.  There are no provisions to upgrade shields.  None whatsoever.  

IpityU - There might be an Artifact that increases shields, but I don't have one in my Vault so I can't be positive. 

Don't know if you know about these already, but here are some things you can do to improve shields for all ships (including commander and prototype) automatically -

1) Building Institution of War (Orbital)) gives all ships +5% shield strength

2) Building the "Ironside Resonance Emitter" adds 10%  shield strength (needs 2 Gigamass to build)

There are probably more, but these are the ones showing up on my ships currently.

This one is pretty basic, but again it impacts all ships - researching various techs on the "Defense" branch will yield various shield improvements

There is a policy that increases all three attack and another all three defense

This begins with the presumption that all Flagships have shields >0   I haven't checked - is that true?

Seems to be the standard for all prebuilt Flagships, Prototypes (I think I have all of them), and Commander (I'm using the Builder set) ships in my game (18 different ships).