Yes, unfortunately Itch does that for no reason from time to time ;-;
At first I thought it was related to how I update the game, but sometimes save files are lost during a period I didn't even make any changes to the game. So I'm sorry that happened to you.
If you can, I suggest you download and play the Windows version, as that way the save files will be stored in your computer. You can also make a new game and interact with the window in Lianna's bathroom to skip to any chapter you like.