3DS:Why not to remove custom firmware

Removing custom firmware (CFW) from a 3DS is not recommended for most cases.

The Short Version

 * It probably isn't why your game is broken.
 * It probably isn't why some part of your console is broken.
 * It isn't going to permanently break your console. The worst that would happen is Luma3DS needs updating (that's the boot.firm file on your SD card).
 * It isn't going to delete all your saves; in fact, it provides tools to back up to make them extra safer than stock firmware can.
 * It isn't going to cause you to get banned on its own. Don't cheat in online games.
 * If you are selling the console, it might be a good idea to remove it then, but you should check first.
 * If you are sending in the console to Nintendo for repair, it might also be a good idea.

Fixing a broken game
Nearly all cases where a game doesn't work is not due to CFW alone. Most commonly, a corrupt game file or a corrupt save file. Removing CFW would it harder to diagnose the problems with a game. What Luma3DS does is expose more details about why a game doesn't work, allowing for more experienced people to figure it out, while stock would only show a generic "An error has occurred" screen.

Another possible case is due to a plugin or mod that is outdated or for the wrong version of the game. In this case, removing the plugin or mod would fix the game.

There are a few edge cases where games can break due to CFW settings. In particular, a few games crash on New 3DS if 804MHz and L2 cache are enabled. Usually these can be worked around by temporarily disabling the setting that is breaking the game.

Fixing broken system applications
Sometimes a built-in part of the firmware might stop working for some reason. Assuming the system was not updated to a point where Luma3DS is currently not compatible, keeping CFW would mean you can fix the corruption, usually with a CTRTransfer. Removing CFW will probably keep the system in a broken state with no way to fix it without ntrboot.

Concerns about bricks
CFW has become exceptionally safe to use on the 3DS over the years, both during and after setup. It is nearly impossible to brick on accident. GodMode9, the most common tool for interacting with the 3DS NAND, requires unlocking writing with a button combination when you are about to do something that could cause damage. The button combination requires deliberate inputs and is impossible to do by accident. (add something about corruption checks)

If Nintendo ever releases a new system update, there is a chance that Luma3DS will be incompatible with it. This is generally not regarded as a brick as it only breaks Luma3DS trying to boot into the firmware, it does not break running other tools such as GodMode9. Usually a new release is made in about a day and can be fixed by replacing boot.firm on the SD card.

The last update to break Luma3DS was 11.14.0-46, released 17 November 2020. The last one before that was 11.8.0-41, released 30 July 2018.

Concerns about data loss
Like mentioned in the past section, CFW has very few risks associated with it, either when setting it up or using it. If you don't delete random files or titles using GodMode9, FBI, or similar tools, you are not likely to lose things such as game saves on the SD card.

CFW provides access to tools to make your own backups of your games, their saves, and the system's internal storage (aka NAND). These allow for better backups than what Nintendo normally allows. For example if your console is ever lost or broken, everything can be manually migrated to a replacement console. SD card data can be migrated if you have movable.sed from the original console, which is inside essential.exefs made during setup. NAND data (e.g. Friend List, Mii Maker, StreetPass Mii Plaza) can be transferred from a NAND backup.

Concerns about bans
Nintendo most likely doesn't focus on 3DS security anymore. Thousands of people use custom firmware on their consoles without issue. The time where a ban is most likely is when cheats are used in public online rooms.

In the past, there was one well-documented ban wave: when Pokémon Sun and Moon leaked online, some people downloaded it and used its online services before release. Bans were given to those who had done so.

Selling console
This is often considered the only real case to remove custom firmware. A buyer may not be willing to accept any kind of homebrew, or the platform may remove listings for modified consoles. Notably, eBay does this if a mention of homebrew is on the listing.

Sometimes a workaround to prevent removal may be to not mention it, but include telltale signs of custom firmware in pictures (e.g. the "Sys" string in System Settings). You may not be willing to risk it however, so removing may be the best option. In this case, you should be careful to not leave remnants that can cause problems on stock, including modified system titles. In particular, make sure the following components work when the console is booted with stock firmware:
 * Nintendo 3DS Camera app
 * Health & Safety Information app
 * DS Download Play
 * DS Internet Settings
 * DS Profile Settings (launching and attempting to enter in a name)

Sending console in for repairs
Nintendo might not like receiving a console with boot9strap on it, so removing custom firmware temporarily would be a good idea. In this case you should make backups of the NAND in the event that Nintendo sends back a new console instead of repairing your existing one.

Keep in mind that Nintendo is slowly discontinuing repairs for 3DS models. As of February 24, 2022, Nintendo no longer repairs the Old 3DS, Old 3DS XL, or New 3DS (non-XL).