Well if PKHeX isn't the problem then what is?
Here are what I think may be the problem:
1. I'm using a physical copy of pokemon sun and I got my save file using JK save manager.
2. The save manager. The file that I dropped into PKhex is called "main"
3. I barely even touched the game. I opened up sun, got my starter, and then wen't to the school. Do you need to be far enough in Sun for it to work?
4. I'm missing a file on my computer that won't let me save as??? I don't really know about this one because I can save as for other programs.
If these don't work than I don't know what will. (I'm kinda desperate for a solution because I would like to use PKHex on other pokemon games as well)
If it would help to see my save file or screenshots I'll attach some.
//--post merged. @Jackletsgo don't double post in the future, just edit into your existing unanswered post--//
Hey um i would like to apologize for my stupidity. I just updated my windows 10 and reinstalled a few corrupt files(powershell) and that seemed to work.