Save files disappearing after update?

It’s as if I just downloaded Citra. My saves were gone and my configs were reset. I was quite surprised about it. Is that really how it works or maybe I did something/need to do something? I’m not too bothered about losing my progress because I look forward to playing it again but I’d still like to recover my saves if possible.

In order for us to provide better support, we need to see the log generated by Citra. This guide will walk you through how you can obtain the log file: How to Upload the Log File.

What citra build are you using? is the folder C:\Users\%username%\AppData\Roaming\Citra\sdmc\Nintendo 3DS\00000000000000000000000000000000\00000000000000000000000000000000 completely empty?
what about the folder C:\Users\%username%\AppData\Roaming\Citra\sdmc\Nintendo 3DS\00000000000000000000000000000000\00000000000000000000000000000000\title\00040000

I updated to Citra Canary 988.

Both folders aren’t empty. In the second folder, there are 5 folders and only one of them has a folder name save_data and has files in them, and those files date back to yesterday when I started a new game on Pokemon Alpha Sapphire.

Then it means that you’ve lost your previous save files. did you uninstall citra, delete any folder or had a power surge and pc shut down while playing?

Nope. Just updated it. I haven’t played for a while.

were you using an unofficial build or citra in a separated folder?

Citra in a separated folder, I guess? I’m pretty sure I didn’t download an unofficial build but I don’t exactly understand what “citra in a separated folder” means.

by ‘separated folder’ i mean downloading an .7z file and extracting in a folder instead of download and installer.

I believe I used an installer since I have it in my files.

it really beats me how something like this could happen, did you login with another user, perhaps made any change on your OS or change anything since last time your save files were intact?

Nope. Just my usual routine, which includes going to the internet, maybe playing a few games, and that’s it. My laptop updates by itself but I just let it do its work and not do anything to interrupt it since I have experienced a problem once because of that so I would never do that again.