The new file is identical to Sh3Gen 0.8.2 except some of the files in the Tracking Room/Template file which reflect the changes I had to make because of the terrain problem.
I never recommend to my users unzipping anything over the previous version any time - but you can do it
Just delete /Tracking Room/Template/terrain.gml afterwards, because it is not needed anymore, but will still be copied into any new map folder, so a lot of diskspace might be wasted.
An alternative is to only replace the Tracking Room/Template folder with the one from the new version - everything else has stayed the same.