I'm not going to say with certainty that is what happened, because there are too many uncertainties to my extremely niché and highly specific situation.
I was playing Command & Conquer: Generals (2003), and it crashes somewhat commonly. It also crashes if I minimize the game more than 2 times. I had already minimized the game once.
I had paused the game and was AFK, when I heard the windows error sound, to find the game had crashed, and WeMod had restarted.
I did not have WeMod connected to the game as it takes up to 20% of my CPU processing capacity(!!!), and I have never experienced the game crashing on me while I had the game paused. It has only crashed either when minimizing or while not paused.
So that is why I highly suspect WeMod to be the culprit for my crash, and consequently much lost progress.