Flames of Vengeance is an add-on to Ego Draconis. You can continue from where you left off if you still have your savegames.
The Dragon Knight Saga is the two halves fully integrated, in other words it's essentially ED+FoV in one package (with caveats); at present it isn't compatible with Ego Draconis savegames and there are a number of additional gameplay changes, mostly in terms of "rebalancing" from what I understand. These may be incorporated into a future patch for FoV.
A number of improvements featured in DKS and FoV are also applied to Ego Draconis when FoV is added on, mainly some visual changes and that the difficulty range now goes lower than "extremely hard"!
