With FoV you will be able to load an existing save and keep playing, or start a new level 35 character at the beginning of the add-on. Hopefully if you were having that much trouble during the end battle you would have saved frequently, and so have a save near the end.
At least for now if you have a digital download version of D2:ED you will need to get FoV from the same distributor. The version in Larian's Vault just works with DVD versions of the game, though they are looking into that and should have something early next week.
Welcome to the forum.