First, you should have kept your backup stored somewhere safe. It is recommended that one keep his or her NAND backup somewhere online, like Google Drive. NAND backups can usually be significantly compressed.So I appear to have lost my nand backup, my hard drive on my pc got corrupted and with it went my switch nand backup.
Im currently on firmware 7 running atmosphere with unburnt fuses since 4.1 due to using Choidujour, can I ever go back to a clean nand?
You are probably unable to return to a clean state without a clean NAND backup. That being said, there's no need for a clean NAND backup if you don't care about playing online. Depending on what you've done with Atmosphere, your NAND might also be less dirty than you think.
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You can try to get ReiNX working by updating your files, but I would recommend using Atmosphere. It has more features and is updated for frequently.Atmosphere for 6.2 works ut reinx not