I had changed the settings so that my PC had 22 boxes instead of 16 so I could have a slot for every Pokemon. I'm using a modpack to play the mod and the pack prompted me to update it, so I did. However, updating caused all of my settings to reset; as a result, my PC was back to 16 boxes. I changed it back to 22 boxes, and all the Pokemon I had in boxes 17-22 were gone (actually, I believe I only had one Pokemon in those boxes). While I didn't suffer a major loss, this will obviously cause problems once I catch more Pokemon later. This may be more or less a feature request than a bug report, but it would be nice if Pokemon in later boxes would save if the amount of boxes decreases.