I've restarted Scorn today after being off for a few days, and lo and behold! Started from the beginning of Act III, even though I had made significan progress in the act.

I selected "load game" and the most recent save was 2 hours and 52 minutes, even though the save slot itself indicates 4 hours and 57 minutes as the toal play time. I quit that save and returned to the main menu, selected "continue" instead, and it still brought me back at the start of Act III. All that sweat for nothing.

Act III only has one savepoint at the very start of the chapter and it is a very long chapter. They apparently fixed this in a patch that is available for the Steam-version, but not for the GOG-version yet (V1.1.8) and added a second savepoint as well as the functionality to continue from the last checkpoint from the main menu. Very much needed QoL addition.

As for me, I lost the progress from Act III because the elevator to Act IV did not work - the "Use"-button did not work anymore and apparently that's a know bug as well. I'll wait for the update to hit GOG as well and hopefully I will be able to continue from my last checkpoint instead of redoing Act III.

EDIT: The patch is out and I was able to continue from my last checkpoint, which was at the elevator in question. After reloading, I was able to pull the switch and descend to Act IV.