Now the question is a lot more clear and easier to answer but before we proceed, there is something that must be cleared up. Updating the firmware doesn't render the game card reader slot inaccessible, at least on higher firmware versions. Updating the firmware does render the game card reader slot inaccessible on lower firmware versions and this could be relevant if a better exploit, such as untethered coldboot, is released someday in the future. To prevent this, the game card reader slot can be made inaccessible on higher firmware versions to preserve its function on lower firmware versions. This all depends on you as there is no right or wrong answer. You must decide if being able to access cartridges on a lower firmware version for a future theoretical exploit is more or less important than being able to play cartridges on modern firmware versions.
Regardless of which you prefer, you must also take into consideration whether or not you want to burn your anti-downgrade fuses. These are preserved for the same reason as the game card reader slot but fuses are easier to maintain. If you want to save your fuses, then it is a no brainer to use Daybreak to update the firmware since it does without triggering them. But if you don't care about downgrading or future hacks, then you can boot Stock and burn them without a second thought. I should mention that there is no advantage to burning fuses since Nintendo does not banned for mismatched fuse counts. However using Daybreak to update the firmware may trigger a ban. So is there a way to update the firmware without burning fuses that won't trigger a ban?
The answer is yes. There are two methods but I'm going to mainly advocate for one. The reason Daybreak preserves the fuses is because while in CFW, it prevents AutoRCM from being erased during system updates. If you update the firmware in Stock even if you have AutoRCM enabled, AutoRCM will be uninstalled before the procedure is done. So if you were to download the system update onto the console in advance while booted in Stock for example then go offline and reboot the console back into CFW, if you install the system update and have AutoRCM enabled, the firmware will be updated without burning fuses. This method is what I personally use and I haven't been banned yet.
The other method is far riskier and not generally advised. Since the method I previously mentioned involves CFW, there is still technically a slight chance of a ban. If you want to completely avoid any usage of CFW and homebrew but update the firmware without burning fuses, you can manually trigger RCM when the system update finishes installing. What this boils down to is having your jig inserted while the Switch is installing a system update and holding the volume (+) button so when it finishes, it will instead boot into RCM. The reason this method is not preferred is because you only have one chance to preserve your fuses. If your jig is not 100% efficient, you will not boot into RCM and your fuses will be irreversibly burnt.
There you have it. Those are all of known methods of updating the firmware without burning fuses. Whether you use any of those methods or none at all is totally up to you. Some people elect to burn the fuses since a new exploit hasn't been discovered since the scene's inception but no one knows what the future may hold.
Thank you for the thorough reply, I appreciate you taking your time and explaining this to me. A few points to note. I am not too concerned going back to a lower firmware version once I update, I am happy as can be to do the tethered coldboot with the jig every time. It's not really a hassle for me.
And yes, you're right, my understanding of the game card reader slot is wrong. I read up on it again, and indeed, certain firmware versions "update" the card reader slot, and going back to lower firmwares afterwards will lead to it being non-functional on those lower firmware versions. I'm not too bothered by it, provided that I can cleanly update and don't have to make use of my NAND backup at some point (which was made on the 9.1.0 FW version).
This is why I would still like to avoid burning any fuses if possible, but again I'm not really sure why I feel that way. Perhaps it's something about the hardware being permanently altered through a software update which rubs me the wrong way.
As for AutoRCM, I don't use it presently. I use the jig and tethered payload launcher maybe four times a year, the switch stays on unless I accidentally run the battery flat. Looking at the AutoRCM option in Hekate is causing me some concern. AutoRCM reads: "
It can restore all versions of AutoRCM whenever requested.
This corrupts the BCT and you can't boot without a custom bootloader." I have only superficial understanding of what this implies. Is the payload I inject when the console is in RCM considered the "bootloader", or what is the meaning of it? I'm hesitant turning it on without a proper understanding of what I'm getting myself into. I know what AutoRCM is supposed to accomplish, but with the warning and my lack of clear understanding has caused me to not consider it. Once I turn on AutoRCM, the console won't boot normally and instead default to RCM without needing a jig.
So now, if I understand you correctly, here is what you're advocating for (given that I want to preserve my fuses for vague reasons):
0. I make sure I am on the latest version of Atmosphere
1. I boot into my stock firmware
2. I download the system update through the system updater, but don't install it yet
3. I boot into Hekate, and enable AutoRCM
4. I boot into "(CFW) sysMMC", and install the previously downloaded update package through the system updater
5. After the update finishes installing, the console will reboot into RCM mode
6. From here, I can inject hekate, and boot all of my different configurations (CFW (sysMMC), CFW (emuMMC), Stock, Fusee)
7. Once everything works, I can disable AutoRCM again
8. Enjoy the latest FW on stock
My apologies if this is pretty obvious and self-explanatory. I really do need to mentally step through this one thing at a time. My worst fear is the switch becoming a brick and being unusable because of something I did with the software. I can handle a console ban (hell, I've been permanently offline for years now anyways), I can even live with a non-functional game card reader slot. Ideally I would like none of these things to happen though, and I get to use the switch on stock to play the games I own online.
Thank you very much for your time, reading guides is all fine and well, but there is no substitute for talking to someone who has done these things before. I also couldn't really find a clear answer in the guide regarding this either. Much appreciated, take care.