Wellp holy sheet , that sounds like a lot of pain, I hope you're able to get rid of it asap.
Meanwhile, the first added scene seems like a nice touch, but I definitely would not want save points to be the only place for saving. That works for the games that sport the feature, but not really in pokemon. Just imagine how many teams you have to train and then not be able to save your game until you find one of these..and then say your game errors or you accidentally close it.. Or if you wanna keep resetting in order to catch something with the nature you want etc, you would have to go back to a save point for that as well. Just feels quite inconvenient for a pokemon game imo, so I'd leave it as it is now. This feature helps people who often forget to save.