FYI The game save is now located under LocalLow/Buckshot Software/ProjectWarlock in your %APPDATA% directory. Registry only saves graphical settings now.
This might actually have to do with the level progression bug. I noticed when I did a fresh install of Project Warlock after deleting the regristry info that I still had all the Single Levels unlocked despite not having a game in progress.
I just tried deleting the save file from the APPDATA folder and started the game up. Single levels were all blanked out. Started a new game and was able to progress past the first Ice Caves mission.
Before the patch I had Project Warlock direct downloaded from GOG.com (not through Galaxy) and had played all the way through. When the patch came out I uninstalled PW but left the registry in place and reinstalled from GOG Galaxy. Despite being a clean install I think the save file imported some data from the Registry because I had no Continue Game but all the Single Levels unlocked and that's when the weird level progression bugs started showing up.
Hope this helps.
yes, if any registry entries exist, the game will import them to the gamesave file if the gamesave file under APPDATA does not exists. That's for your convenience so that you won't have to start all over again - although the "registry" progress won't be updated when playin on 126.96.36.199 and above.
If you want a complete fresh campaign - you have to remove the APPDATA and Registry entries.