Not directly. You'd need to back them up with SaveDataFiler, then restore them again after you've installed them to your homescreen.
A member created it and posted the link in the thread some time back. It's the "official manual", well until another major change is made in a nightly and it becomes outdated anyhow.
The icon is there but when you press it you're prompted to perform a system update. It usually occurs when someone has a launch day 3DS that has only ever been updated with game carts (they don't come with eshop/browser updates).
- Launch the Gateway Menu with Cubic Ninja
- backup your NAND, copy the resulting nand.bin to your PC and make a backup of the entire SD card too.
- Reload the Gateway Menu and select setup emuNAND. This formats your SD card (which is you needed to back up your SD card).
- Copy your SD card backup from your pc to your SD. Done.