Sometimes you need to upgrade your console, upgrade the firmware or upgrade Atmosphère, using the @l7777 's guide (https://gameparadise.org/tutorials/updating-hekate-atmosphere-and-hos.191/) as base I hope to crease a list of necesarie steps to sucessfull upgrade your console.

Make a backup.

Always make a full backup of your console, so if something goes wrong you have a know working restore point.

If you are going to update your SysNAND you can create a backup using Hekate's NYX, It's the easy way.

For your EmuNAND there are two paths:
  • If your EmuNAND is RAW based, you can use a tool like EmuTool (EmuTool GitHub) to backup the RAW partition to a set of files on your PC. That backup can be used later to restore the RAW partition or you can convert your setup to File based EmuNAND using that files.
  • If your EmuNAND is file based, making a backup is so easy as copying the
    SDMC:/emuMMC
    folder to your PC.

Also is advisable to backup all files on your SD Card, You can Use Hekate's UMS for that task, so you don't remove the SD from Console and avoid the problem associated to manipulating the SD card.

Preparation.

Before you start the process you need some steps:
  • Download latest Atmosphère files, download again from the GitHub repo no matters if you think you have it, sometimes the repo is silent updated.
  • Download latest Hekate files, download again from the GitHub repo no matters if you think you have it, sometimes the repo is silent updated.
  • Download latest Sigpatches from the GBATemp Thread no matters if you think you have the newest, they might be upgraded.
  • Download latest Sys-Patch Sysmodule some people tells is redundant but is better be safe than sorry
  • If you are going to upgrade your firmware, remove any theme you have installed! NX-Themeinstaller now have a option to remove all installed themes.
  • You can get a legally aquiered firmware files, by example dumping them from another console using homebrew like https://github.com/mrdude2478/Switch-Firmware-Dumper or DBI, also a search engine can help you to find a correct backup, by example Firmware 18.1.0 rebootless have an ID of e7e2b68
Starting the process.

Restart your console to Hekate's NYX and load UMS tool, or remove the card and put on your PC, is up to you, Hakate may be a little bit slower but you do not risk physically your console.
  • Delete
    SDMC:/atmosphere/contents
    or
    SDMC:/atmosphere/titles
    , you should have backed up this folder before.
  • Delete the next folders, that's because the first time you load new Atmosphère that folders will emptied and that can take a lot of time so you could think your console got frozen, so in order to avoid that false alarm it's better to delete them before start console.
    • SDMC:/atmosphere/crash_reports
    • SDMC:/atmosphere/erpt_reports
    • SDMC:/atmosphere/fatal_reports
  • If you had used INCOGNITO_RCM, is advisable to remove incognito from yours *NAND, having PRODINFO blanked via Incognito RCM can create problems on the new firmware/atmosphère versions.
  • Extract Atmosphère zip file and copy to the root of your SD, overwrite all files.
  • Edit your
    SDMC:/exosphere.ini
    file and add/change the next values to «1» in order to enable Atmosphère incognito on telemetry:

Code: 
blank_prodinfo_sysmmc=1
blank_prodinfo_emummc=1
  • Enable DNSMiTM, by editing the
    SDMC:/atmosphere/config/system_settings.ini
    and be sure the parameter
    enable_dns_mitm
    have the value
    u8!0x1
    :
Code: 
enable_dns_mitm = u8!0x1
  • Extract the downloaded Hekate zip file, and copy to the root of your SD, overwrite all files.
  • Upgrade your payload.bin file, if you use a injector on the injector, if you use a modchip replacing the file
    SDMC:/payload.bin
    file, if you use Hekate rename the file
    hekate_ctcaer_X.Y.Z.bin
    to payload.bin and copy to root of your SDCard.
  • Extract the sigpatches file and copy to the root of your SD Card, overwrite all files.
  • Etract the Sys-Patch zip file and copy to the root of your SD Card, overwrite all files.
  • Create a folder on your SD Card and copy on it the extracted files for the firmware.

Testing the console

Put the card or turn off the console, then start your console as usual and let the HOS to load.
If everything load fine yu can now upgrade your firmware or go to next step.
In order to upgrade your firmware, load Homebre Loader (HBmenu) and run Daybreak. it's better to select «install (FAT32 + exFAT)» option, on this way if anytime you insert a SD card formatted on exFAT you will avoid an error. This option only install additional drivers but DO NOT modify your card. Be sure of select «Preserve settings» if you like to preserve your games and configuration.
Your console will restart once the process end.
Test your installed titles and verify some games to run OK.

Finishing the setup.

After you know your console boots correctly and everything is fine now you can reinstall SYSMODULES, cheats, and modifications. you can choose restore them from your
SDMC:/atmosphere/contents
backup or I do recommend to look if there is any newer version.

By example you can use the post TESLA and Overlays to find the most recent version of Tesla and overlays, also if you like there is a tutorial for build the latest code available https://gameparadise.org/tutorials/how-to-build-overlays-from-code.227/, it's for advanced users.

Other common SYSmodules are, Emuiibo, Mission Control, FTPD, etc.

Remember to restar your console once you upgraded any SYSMODULE

Take a time and look for updated version of your Homebrew.

If you use themes look if there are new versions of NXThemesInstaller and the patches needed to install them, after update all components, reinstall your themes.