Problem with secure values

I've run into the issue where the secure values on my Pokémon ORAS file now differ and refuse to load. I've been searching this forum for various clues & used a few programs but I'm stumped. I've got no background in software editing and such but I'll try to be as complete as possible in describing my problem.

I've been using Save_Manager to implement my PkHex-edited files into my digital copy of Pokémon ORAS, always being very diligent to backup & import my data in order. Alas, a few days ago I f'd up and skipped a step (complete story in the spoiler below) causing the secure values to not match anymore.

I've tried the following things:

• Attempt to edit secure values in PkHex, alas were greyed out so no dice there;
  
• Searched the web and this forum to find https://gbatemp.net/threads/antisavegame-restore-secure-value-updater-ps-acnl-prw-ssb-xy-oras.396644/ and tried to manipulate the content this way. I was able to find a .sav file (named 00000001.sav) on my SD card in the directory where Pokémon ORAS (namely Nintendo 3DS\c7ed3bf11decd9439ce5e6b8240a383e\9bd200ea47800056534c303800035344\title\00040000\0011c400\data) was stored. However, 00000001.sav's file size is 1024 kb while the save file used with the PkHex software (named "main") is only 472 kb. The program did prompt this discrepancy, but pressed on anyway. To no avail as the familiar error was still there.
  
• Moved on to the next recommended program: SVDT. Installed and opened it up, but was unsure how to continue after allowing the program to rewrite secure values by press "A" (see first spoiler below). I had no clue how or what I was supposed to transfer or overwrite once I was in the program and on the main menu (see second spoiler below)
  

Other information: Pokémon Omega Ruby is the only game I've got installed and is a digital copy. I'm using a 2DS system.

Any help would be greatly appreciated. I tried to search high & low for tutorials but came up short (aside from a single video in Italian, which I don't speak). Many thanks in advance!

Okay,

If you have Savedatafiler, at the page where you can extract your save,

While hovering over the game, instead of extract, delete secure value.

That solves the issue.

Thanks for the reply. I don't have Savedatafiler but I'll see if I can hunt it down and fix the issue that way.

Much appreciate the assistance.

Thanks for the reply. I don't have Savedatafiler but I'll see if I can hunt it down and fix the issue that way.

Much appreciate the assistance.

No issues!

If your other apps have the delete secure value option, you probably could just use that too

jksavemanager automatically deletes securevalue, but that's for cfw only. There's a way to delete secure value from *hax, but the app hasn't been released yet (the functions are there in ctrulib, but nobody has gone and publicy used them).