Quite a lot; the data telling the game to take you to all of the new battles is in flevel.lgp, so you won't be able to fight enemies like Locke, Venus and Theo. IIRC, armorvil had a problem with the game crashing in the first reactor when he used the the scene and kernel files with the PSX version, because there was a new enemy in there (although that may have been because he didn't have the battle.lgp file). This mod uses quite a lot of field edits, so you might miss out on quite a lot.