Is boot.dat on the root of your SD card?
Install them using SX OS' built in title-installer or use Tinfoil.
Basically the Switch has pretty bad exFAT drivers that when combined with homebrew make corruption an inevitability. The corruption can occur with FAT32 as well but because it has a backup, you will never notice it on the Switch but your computer may pick up on it. If you want to avoid corruption as much as possible, only close homebrew applications by using their respective exit buttons; do not exit homebrew by using the Home button.
- You can backup the NAND with or without games installed into the internal system memory. The only difference is that if you try compressing the NAND after you dumped it with content installed, it will be slightly larger than if you had no content installed.
- Not sure what you mean by risk. It is completely safe to do a NAND backup regardless of whatever content is on the NAND.
Firmware updates only update the SYS partition of the NAND. The only other difference between a normal system update and one with ChoiDujourNX is that official system updates remove AutoRCM while ChoiDujourNX lets you re-install it after the firmware is updated.
Correct
as long as you are using AutoRCM to turn off the console because booting into non-RCM OFW will burn fuses.
Hekate is a payload that doubles as a bootloader. Once in RCM, you cannot turn on the console by normal means hence the need for a bootloader. CFW are files on an SD card that cannot be loaded by themselves; they need a bootloader to patch the firmware so it reads those files. Hekate can also now load any CFW you put into it besides Atmosphere either by configuring it under launch configurations or by using Hekate to launch their respective bootloader to load their CFW (e.g. ReiNX or SX OS).
If you don't mind having the second console risk a ban, there is no problem.