Designate Flagship

[Vanidas]

When you hover over an Admiral in your leaders tab, it tells you the leader is commanding a specific ship in that fleet, meaning it's the flagship. Other than building the flagship first, is there any way to change the flagship of the fleet?

[Half Phased]

No, but it doesn't matter, an admiral will move there flag from ship to ship as they're destroyed, only dieing once there are no other ships to move to. And it's not like flagships have an impact on fleets anyway.

[Helican]

It really doesn't matter. There is no mechanic in the game that has any impact on that whatsoever.