The game can't delete saves without manual input. The only way saves can be deleted is:
1. If you're on PC, Linux or Mac then the save in the game folder AND the backup folder (stored separately on your HD) have to be deleted
2. If you're on Android then deleting the apk will also delete all saves
3. You hovered your mouse over the save file, hit "del" on your keyboard and then said yes
If none of these things happened in your case then you might want to make sure that you're on the correct save page (click on the numbers at the bottom of your save screen) or load an autosave (click on "a" on the save screen - it's on the far left of the page numbers).