To delete the files in the dynamic folders, browse to the folders in Windows Explorer and delete the files in them, but not the folders themselves.
'..\Beyond Divinity\Acts\Act1\Dynamic', '..\Beyond Divinity\Acts\Act2\Dynamic', etc.
These folders are used as a cache for the game. Files are created / copied there from the save game folder when you load, and written / copied to those folders when you save a game. The files will be re-created as required the next time you start Beyond Divinity. If there was a corrupt file in those folders, deleting the files should fix the problem.

If the alchemist is still stubborn after that there is probably a workaround to get him talking, but I'm not sure about the passive enemies (the patch fixed one cause of that, anyway).