If you have a modded game and you want to continue playing it to the end, you'd better skip the update for now. It will overwrite most of your files and you must start a new game.
Hopefully you followed the instructions to have your modded game version separated from the GoG/Steam/Beamdog version.
EE/EET Mod Setup Tool
in Enhanced Edition Trilogy
Posted
If you have a modded game and you want to continue playing it to the end, you'd better skip the update for now. It will overwrite most of your files and you must start a new game.
Hopefully you followed the instructions to have your modded game version separated from the GoG/Steam/Beamdog version.
You find many useful hints in this discussion:
https://www.reddit.com/r/baldursgate/comments/8unf15/baldurs_gate_ii_enhanced_edition_25_patch/
As a main rule: do not patch an ongoing game.