Was pretty bummed out by restarting the game, but I did not come that far, and with the fast forward dialog button it was pretty easy to catch up again, playing it now around the same area I was before within like 2 hours so it was no biggie. If anyone else has this problem then they can always try the DLC method first before reinstalling the whole game, but the only thing that worked for me was to reinstall the entire game, maybe it's just me.
Regarding just deleting the DLC cia and installing it again without pressing the add on button, been there done that multiple times but never seemed to work, at least for me. I did use checkpoint, but once I deleted the game from freeshop the checkpoint save disappeared. If you have your save saved on the sdcard, reinstall and it still doesn't work, then you most likely need to also delete your save while reinstalling both DLC and the main game, but as I have not tried this method with keeping my save, it's a good tip for anyone of you that have already put in hours into the game. If you just scroll down you will see the sdcard saves pop up, try to save before reinstalling the whole game, as I did not know this it made me play through the whole game again when I ALREADY put 6 hours ish into it. If anyone tries to do the same thing, make sure that you have your save saved on the sdcard, and not on the 3ds itself. You will first have access to your DLC items when you enter historia, so you need to play through a little bit. Downloaded the dlc immediately after and then played through the game a bit without pressing on "add on" button in the home screen.
I uninstalled the whole game, and redownloaded it. It looks like when you click that button, the game checks for the validity of your dlc, and when it sees that you have pirated the dlc, it makes it unplayable or something like that. As i feared the problem was the "add on content" button i clicked earlier.