When you opened Data Management your system switched from being in emuNAND to sysNAND no cia's were uninstalled.

If you followed through with the a9lh guide you are likely booting into sysnand, and unless you formatted the sdcard at some point you should still have your emuNAND on there.

Boot while pressing 'select' and tell luma to 'autoboot emunand' or deselect 'autoboot sysnand' and see if that gets your cias and saves back.

 

Did you make a nand backup of your emunand?

 

-snip-

@nekojosh Your 3ds is booting sysnand. Hold select on 3ds boot and turn off "Autoboot sysnand"

 

Ok, so to address most of the comments:

1. I'm not booting SysNand but Emunand, I had it set so it boot that way by disabling the auto boot in Luma.
2. I've yet to have any issues with RxTools but don't have a particular reason to keep using it hence why I was trying to move to Luma but when booting the emunand and reinstalling the games save files seems not to be there.
3. I did make a nand backup of my emunand but it seems that didn't help since when I restore it and boot the emunand I see all the slots there for where the CIAs used to be but there are no longer there... I did open the Data Management on emunand, also on sysnand while trying to setup Steelhax since it installed the update which I had to manually remove.
4. No sure about injecting EmuNAND into SysNAND, I've always felt safer having them separated.

I'd like to get the save files from at least 2 games which are Smash bros and Bravely Second, the rest I don't care much.

On my SDcard I have all the .sav files on the root and when I access the Nintendo 3ds folder I have the following structure:

/Nintendos 3DS

/2d229bfb4548765a24f9fe0a4464aceb

/89fe00eb4780038c534c363400035344 (This one has 2.99 Gb which is where I guess Pokemon Moon was reinstalled but there is no save file there)
/114e00c43110b01e3030303000284245 (This one has 11.8gb which is where I guess everything else used to be but can't seem to be read by current emunand​

/37a1b4a3520773446cbf55a7e3756f78 (This I guess is from sysnand since it is only 11.9mbs and there is nothing installed there)​

Any ideas on how to fix this? would just copying the content from one folder to another fix it?

​

— Posts automatically merged - Please don't double post! —

Lol seems like I solved it myself coping the contents from one folder to the other fixed it.

 

Thanks everyone for your input.