Replacing the files with default folders didn't work, and reinstalling didn't work.
To reinstall, I simply backed up the required files then deleted the rest, then ran the installer and started FH before I put the backup files back. Even starting the newly-installed FH didn't work.
Sorry for the late reply, I had to go before I could try to fix FH.
Editing to say another thing I found out about this glitch: Only custom maps have the default trees and rocks.