Darkfyre

Alrighty then, after returning to the game after quite some time, I noticed a few things missing. First and foremost I was pretty sure about quitting somewhere in Hoenn and yet here I am between Johto and Kanto with Youngster Joey still standing around here. The rattata I trained is missing and the Gyarados is set back some levels too, both were used in this particular fight. Also those two police dudes wont let me enter Mt. Silver, although Im sure that I beat both leagues. Some items are missing too but thats not too important. Story content was also reset to some extent (That police guy in Cerulean City had to check for my second badge again?)Im just really confused about all this. How did all of this happen? Why are only those things missing? What if that happens again? I dont really care all that much about getting things back, im more concerened about wheter Im remembering those things the right way. Is there some way to check the data? I already read the guideline and the first Support pages to check for similar issues but I saw nothing that describes my own predicament. My Kanto and Jotho pokemons are still here as far as I can remember at least. Man, this is just really confusing and my main concern is to figure out what exactly happend. Maybe im just going crazy.