@theSLAYER Frankly I don't know all that much about this stuff. I actually didn't know you can access the main file by simply right-clicking that. But doing that now I actually realize what may or may not be the problem. You know when you search %appdata% and go into the Citra folder that's located there, eventually you'll find the main file you're looking for? Well I copied and pasted the Citra folder into the ''Games'' folder I created (simply located in Documents) where I try to keep things organized so I can easily find files, and within the Citra folder I renamed some of the folders to recognize certain games faster.
For example:
C:\Users\Rens\AppData\Roaming\Citra\sdmc\Nintendo 3DS\00000000000000000000000000000000\00000000000000000000000000000000\title\00040000
In the 00040000 folder there's 4 folders, one for each game (Sun, Moon, Ultra Moon, Omega Ruby) but they're all just a bunch of numbers, so I renamed those by putting the game titles after the numbers. Every time I click Open in PKHeX the 00040000 folder with the four other folders in it is where it opens.
But I just did the right-click way, and it opened to the same four folders, but the original un-renamed ones in the original Citra folder that I copied. And the Omega Ruby main file in there seems to be an earlier save (last modified at 8:25PM instead of 9:00PM, the 9:00PM one being the file I've been messing with on PKHeX).
Do you think the root of my problem is the fact that I copied & moved and renamed some folders? Sorry about this, I tried keeping it short, but maybe you know right away if this is the case or not.