How to remove dead NCA's and save games

[DemanNL]

So I decided to migrate from SX OS to Atmosphere. However, for some reason SX OS has been installing quite a bit on my internal storage it seems (only 10GB internal storage remaining). During the migrate I was unable to migrate the emunand, so I created a new one.

However now when I check my system memory using tinfoil. I see a lot of NCA's in "system:/Contents/registered". I also see quite a bit of save games in "system:/save".
I checked data management in the new emunand, but it's empty because I have nothing installed. I also checked stock NAND, however the data management seems quite limited on 4.1.0 and I am unable to see why around 20GB is in use, apart from like 4 save games.

Anyone have any idea how to clean up unused files in "system:/Contents", "system:/saveMeta" and "system:/save" ?

I do have a backup of my original NAND containing the following files: rawnand.bin, keys.txt, boot0, boot1, boot.data, biskeydump.bin
So I guess restoring original NAND is an option?

 

[DemanNL]

Ok, so I have decided to solve this by using my old NAND backup. Restoring my old NAND backup and making a new emuMMC resulted in internal storage having 24gb of space free. I hope installing games using tinfoil on emuMMC puts it in the proper folder and will avoid future problems.

But I couldn't find any other solution than just restoring everything.

 

[Draxzelex]

Ok, so I have decided to solve this by using my old NAND backup. Restoring my old NAND backup and making a new emuMMC resulted in internal storage having 24gb of space free. I hope installing games using tinfoil on emuMMC puts it in the proper folder and will avoid future problems.

But I couldn't find any other solution than just restoring everything.

Some title managers support deleting orphaned .NCA files like Goldleaf.