If you have a custom theme installed, make sure to uninstall it (via
NXThemesInstaller) before you proceed to update.
You can backup your saves with
JKSV and restore them after the update should you need it.
Before you update firmware, make sure that both
Hekate and
Atmosphere support the latest firmware or the firmware you're updating to.
If they do, check if the
sigpatches are updated to support the latest firmware and Atmosphere version.
If everything seems okay, update Hekate and Atmosphere first, followed by sigpatches.
Once you do that, update firmware via Daybreak as well. You can find firmware files on that certain site we aren't allowed to link to (that's what I usually do) or you can dump the latest firmware after you update your OFW. I personally like to keep my OFW firmware version the lowest possible just in case a future exploit is found and supports the firmware I have (unlikely to happen, but one can never know).
If you used either Haku33, TegraExplorer, EmmcHaccGen or ChoiDujour in the past, you might run into a
save issue after updating to 17.0.0 or newer. To fix it, make sure to boot at least once into sysNAND CFW with Atmosphere 1.6.1 or newer.
If you've used Incognito_RCM or similar in the past in order to blank your prodinfo, Atmosphere will crash as soon as your console connects to the Internet and tries to connect to the Nintendo servers due to your console not having valid prod keys.
You won't run into this issue if you are always in airplane mode or if you're using
DNS MITM.
If you plan on connecting your console to the Internet, you can use
this patch and/or DNS MITM.
I guess I've covered everything for now.