Problem with Hakchi Folder Structure and Save States

[/classicSNESmini]

So I had my SNES Classic set up to switch to the NES Classic to play the NES games, but I decided to get rid of that cause the switching and rebooting was getting tiring.
I eliminated the links to the NES Classic, added my NES roms to the folder structure and have them how I like them. But now my save states are completely gone. I panicked last night, thinking my 6hr+ run of ALTTP was gone.
I looked through the save state manager, found that all my states came up. Great. So I followed the guide to transfer from the save state manager into the Hakchi Saved folder on my USB. Ok, phew, that worked... But I lost my folder structure...
Wtf...
I'm just confused, frustrated, and probably overlooking something really obvious. What order of operations should I be doing to keep my folder structure, and maintain my save states?
BTW, when I "export games list to usb" there's an option that I CANNOT UNCHECK to "create saves folder". This may or may not have something to do with anything. But I don't know.

submitted by /u/rbarton812
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