I was looking at your source code, giving some unused parts of it a GUI in my editor, and noticed something about how the save file must store Pokémon. There's the regular section, storing all Pokémon as shown in Chimecho's, which I believe is overwritten by the active data (PkmnEx) upon leaving the dungeon. I believe the PkmnEx/Active Pokémon data is only read once per floor. Using the Active Pokémon Storage classes to edit the kind of Pokémon only changed when I went the next floor of a dungeon, rather than when I loaded the quick save. Also, the PkmnEx class shows I have full health (44/44), when I really have 7/44. There must be a 3rd area where this is stored, specifically for quick save. Perhaps that very bottom save slot, the one after the first redundant two. I might look into this later, I just wanted to put this out there.
Oh, and I am impressed with your BooleanBuffer class. It makes things so much easier to find (whereas I initially tried to do complicated bit shifting to bytes). Because of that and the additional features you decoded yourself (structure of Pokémon and adventure log), this thread is now stickied in place of mine. Well done, matix2267! (Perhaps now I'll be motivated to make even greater strides in my program, for the good of all of us, and so I can justify sticky-ing mine again.)