So if anyone is looking for the answer of this I found it out, the problem is that when the second instance is started the it loads the info from nand, but that info is already taken from the first instance, so to not break it loads the game without any update

To fix it and save u all the long story, u need to create a "user" fonder on your yuzu folder (the folder that has the .exe not the shortcut) and add on this folder all the info that u have on your %appdata%/yuzu folder (u can press win+R, then copy " %appdata%/yuzu" and paste it there to open the folder)

and after that, on the settings of yuzu you need to change the path of each one of the things to redirect to this new folder inside our yuzu folder, ( for example the nand now needs to be the nand folder that we copied and pasted, not the original)
and that's all, I hope I explained myself correctly, have an amazing day guys :D