To stop your save from deleting itself, right click -> settings. Select storage if it's not already on that tab and move the scroller all the way to the right (unlimited storage) and it wont delete your save anymore!
This is because flash will only store as much data as you tell it to!
The problem with final fantasy is that it has headed in a really horrible direction. This glorifies the brilliance that is the earlier work of square enix, with his own twist. This game is absolutely brilliant and I would not change it for the world.
IMPORTANT: If you are losing your save files, right click inside of the flash object, click settings and set storage to unlimited. DO NOT LOWER IT AS YOU COULD LOSE MORE SAVES. This is due to kongregate saving too much cookie data on your computer because of the memory limit. I feel your pain.
I much approve of this sequel. (y)
However, I would like to see an option to turn off auto-regeneration when outside of battle, it makes the game too easy. :)