If you play the downloadable version for PC, your saves should always stay in the game folder. If you play the browser version tho, sometimes the saved data suddenly disappears. I have no idea when and why this happens, so there isn't much I can do, sorry. ;-;
At any rate, to alleviate this issue I added a feature that lets you skip to any chapter in the game by interacting with the window in Lianna's bathroom. You'll get a boost in levels and money too, but have to redo any side quests. I hope that helps and you have fun!