After finishing Earth Tower (EX-R), going back to the Water Tower (Tokiko Feathers) will soft lock the game.
Point of no return is 1 screen before Water Tower Area 1. Backtracking after this point or going all the way through the tower will revert the game to the Earth Tower storyline.
Game reverts to only Earth tower being accessible, and the human village event with Aya being inaccessible.
Game is now soft locked. No storyline can be completed. Trying to replay the Earth Tower storyline leads to a freeze before the boss fight.
The following may or may not be related to the cause. The game can't make up its mind about whether or not the treasure chests have already been opened: the 4 blue chests inside the Water Tower and 5 wooden chests outside the tower are unopened. They will all be open when backtracking. Additionally, there is a red chest outside of the tower that is missing. It will reappear and be open when backtracking.