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).