Looks like immediately after resetting the game, the auto-save feature stops working. Reloading the game fixed the issue for me. Just wish I realized what was happening sooner. Either way, awesome new update. It's a step in the right direction for keeping the game going for quite a while.
I recently upgraded my Flash Player to "WIN 10.0.12.36" and now my save data is gone. Also, the menus and battles are EXTREMELY laggy after upgrading to the newest flash player. So much so that I've died because I ended up healing wrong people, or I wasn't able to use defense abilities and so on. Perhaps another update to the game is needed to compensate with this new flash update.