Twice now I've lost my FF2 "Resume Game" and it starts me back at Level 1 all over again. The first time I had almost beat it (around level 55 or so). My daughter was also playing it and asked me why it started over again for her as well.
The game menu shows you can do "Story Mode", "Lite Mode" and "Time Attack". My educated guess may be something like this: You can only have ONE saved game (not one per mode). If you start one of these modes, DO NOT start any of the others unless you risk losing your existing progress. I think Feeding Frenzy 1 was also like this, but I think it at least warned you about it.
You do NOT get a "Resume" warning or a notice that you might lose any existing progress if you switch to the other game modes. Personally I think this is stupid -- there is no reason why the game couldn't save three game types for each of these. They SHOULD be considered separate entities. If this is indeed the case, then this is a bad bug -- Data Loss. I would be losing my save info without being told why.
I also fear losing my single-player progress if I choose to play in Co-Op mode, but I haven't confirmed that yet.
Has anyone else mysteriously lost their FF2 progress, or has more info on why this is happening?