If it means anything, THIS was a big surprise to me too! I haven't heard of any of this until you said it.
What exactly did you do before it was deleted? Where was the save file?
In my first time was right after we got captured by the bandits, i saved, went to sleep, came back the next morning and boom, my save file were gone
The second time was right after we meet the weird wizards that turns the ex-bandit baddie into a slime, i saved, went to sleep BOOM save files (yes plural) gone
Im really mad right now bc it took me a long while to get there bc im not good at stealth and thr fights are kinda hard
I am very sorry about that and VERY confused myself. Losing a save file right after the bandit baddie scene is disappointing.
Sadly, I don't know why this is happening myself, like I said I never encountered this before. If anything, if you plan on playing through again and getting to the same place, open the game's www-folder and go inside the save folder. Then copy over the saves in a different folder seperate from the game's one, or see if the save files/folder magically disappears after you close the game.
Again, sorry that I can't help more than this and I'm sorry your first experience here was like this.
I still hope you enjoyed the game between the save corruptions!