There are actually two storages of saves for renpy games like this one; first is in the actual game folder, next is in the hidden %appdata% folder in the Users in your main drive (y'know, where it's usually named as your pc user profile). If you deleted the saves in the actual game folder, the saves in the %appdata% folder usually has backups of it and it will show the saves (unless if you delete those saves in there too).
Kinda confusing but I learned this when I was playing another renpy game called Tavern of Spears. Idk if this answers your concern tho...