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So...question.
I backed up my save to the computer, messed with my boxes in PKhex, overwrote the save on the SD card, booted up the savemanager, pressed the button to import the save, screen went all missingno. for a split second, then I was at the homebrew screen again.
Reset DS, launched (physical) Omega Ruby, but my save was untouched (as if I had never used Hex)
What did I do wrong?