They are not lost if you did not uninstall the old version before installing the new version. If you uninstalled the old version, then they are all lost.
There was a change to the full game installer though. It will force the installation into a folder named "Aces High III". If your original game installation folder is not named that, then look for the "Aces High III" folder in the original game folder. That is where the game is running from.
If the above is true, then copy your old "settings", "skins", and "ah3terr" folder to the new installation path.