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Updating does not remove your CFW. For quite a long time, Luma3DS has blocked attempts by updates to overwrite the FIRM partitions, the little bootloader things where the B9S entry point code to run Luma is stored. Definitely update Luma to the latest 12.0 before you update the console. Some old versions of Luma just throw errors if you update to the newest firmware. If your SD card contains boot.firm, just drop the boot.firm and boot.3dsx from the latest Luma zip there, overwriting the ones on the card and you're set. If you have arm9loaderhax.bin instead of boot.firm, do this stuff to update from A9LH to B9S.
Yup, just paste the latest Luma boot.firm and boot.3dsx and you're ready for system update. Bank itself you can get from the eShop. If you have any plans to import Pokemon from gen 5 DS cartridges (or ROMs via Dream Radar Cart Redirect) or gen 1-2 VC games, be sure to pick up Poke Transporter. Since the eShop doesn't list it and you only see the button to open the eShop page to download it after you pay for a Bank subscription, you can either get it from hShop or use this tool to open the eShop page directly to get it.