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I don't think you do understand, otherwise you wouldn't be calling it a bug.I can understand that but still it's annoying. It's a good idea to setup your sysNand Home menu and emuNand Home Menu differently so as not to confuse the 2 when updating the system. For me I made 3 extra folders that say SYS for sysNand and EMU for emuNand. I put them on the bottom left as I have 3 rows.
You should be able to backup the emuNand partition using most partitioning software. This would make recovery much quicker.
The 3DS always reboots when leaving the settings app, even when you exit it from sysNAND.











