how to rebuild destroyed flag ship?

Reload saved game & be more careful     Once a Commander or Prototype ship goes into the black it can't come back.

You can design a new Flag Ship, but if you are at your limit of two, you won't be able to build another one. This limitation should only apply when you still have both of your Flag Ships. You won't be able to build another one if it is one of the ones you get from culture, Command ships, or other sources. Those are considered prototypes and are lost forever once destroyed.