There are differences between having D2:ED + FoV and DKS. Any changes made in DKS (like changes to they flying fortresses, enemy placement, quest experience to make leveling faster at the start of the game, etc) which would break save compatibility were not included in FoV, though some graphical improvements, etc, will be applied to the D2:ED section. There were no quests or areas added in the D2:ED section of DKS, but additional sets and unique equipment were added, and changes to enchantments (also used by the random item generator) and some of the skills effect gameplay.
There is a (large) conversion patch which will update D2:ED + FoV to be the same as DKS, though any existing D2:ED saves would not be compatible after it is installed.
Unless you really want to continue with the same character, rather than re-create a level 35 character at the start of FoV, it may be cheaper and easier to get DKS rather than FoV (especially with the occasional Steam or US Amazon sale).
Next month there will be a Divinity Anthology released (see
Gamescom 2012), containing Divine Divinity, Beyond Divinity and Dragon Knight Saga.