Your save file will be compatible, so you can simply proceed from where you left off. If you downloaded v2.00, please download v2.01 just in case (patch over a vanilla WOTL ISO and replace the previous version in your game collection). I'll post a reply explaining the bug in more detail for those who are interested. I normally wouldn't do a full post for an incremental update like this one (from v2.00 to v2.01), but this one has an important PSA: there was a rare but nasty bug in v2.00 that could prevent you from starting the side quests in chapter 4.
My QoL mod for War of the Lions has been updated to v2.01. If you want to opt out of that feature, you can redownload the archive (it's still v2.01) and use the patch file of your choosing to turn on or off either of the two optional features! Nothing else in the mod changed, so if you're happy with Smart Encounters turned on, then you don't need to take any action.
EDIT: Multiple people requested that I make 'Smart Encounters' (only fight random battles when you want to) an optional feature, so I have done just that.
