For anyone having problems with progress due to a possible bug, you can try releasing some glitches. In box 2 and 3 there are a few glitch invisible pokemon which for whatever reason represent a checked flag. Not every flag in the game is in there, but it seems some hacked-in flags are there. These are actually completely invisible pokemon named bad eggs, but they can be released. There are also a couple of bad eggs I had in my final game. To find these invisible flag pokemon, just drop a pokemon and scan through the box. Release them if you feel like it. They aren't really game-breaking flags to re-enable. Withdrawing these pokemon and viewing them through your menu will give a glitchy restart. I fixes professor oak blocking the stairway by doing this, and retriggering the ending texts and cutscenes etc. it doesn't reset any pokemon unless they're part of the script. I hope this gets seen and upped so people can read it for this awesome hack. Good luck, have fun!