Another day another question.
I expanded Emerald's trainer list recently. Thing is, the game has been acting very...weirdly due to this. Trainers beyond the old limit have cleared trainer flags, as if they've already been fought before, which is weird, because obviously, you've never fought them before in an unedited game. They act as if they've already been battled when you definitely haven't.
But it gets stranger. Stranger danger.
I went ahead, thought nothing of it, and just used settrainerflag on all the trainers I needed, but this had very adverse effects on the game. Setting certain flags apparently altered the game's events. After setting the trainer flags for a range between 35X to 3CX for instance, the game started acting as if it were still in middle of the Kyogre/Groudon spat, where their weathers conflicted with each other. Yet, nothing was going on in Sootopolis, Sky Pillar still lacked Rayquaza, and most other things were fine. There was even rain in Evergrande. Not to mention, it wiped the player's badges, and even reverted your menu to that of what you had when you first started the game, even if you had already beaten it.
Is there something wrong? I need to know, what sort of relations do trainerflags have to do with events? Maybe I'm just not supposed to have any more trainers in Emerald then what it provides me with...