Hmmm, it sounds like you didn't save something, or you have moved some things around within the game folders. Are you sure you didn't move any of the object groups around in their folder within the FH folder?
And, reinstalling FH WILL make you loose your maps, UNLESS you back them up. Just go into your "Terrains" folder, and drag everything onto your desktop, do the same with your "exports" folder. Then you may uninstall and reinstall FH, and simply copy all the files and folders you saved into their same places in your new FH folder.
I hope it all works for you!