I'm sorry to hear that :( The fairy glitch is annoying but if you avoid it you should be able to save normally from the menu (unless there is another bug I don't know about lol).
If your save data got corrupted by the fairy I can fix it if you send it to me. But in any case, an updated version of the game will come out very soon and it improves on many aspects including bug fixes like that one. People should probably wait for that one :P
Thanks for sharing your thoughts.