You can do this, but you could also just copy your emuMMC from one SD card to the other.
Your users and saves on your sysMMC are stored on the sysMMC, so they will be preserved no matter what you do to the SD card.
For the users and saves on your emuMMC, you will probably want to transfer your emuMMC from one SD card to the other, since the users and save files are stored on the emuMMC. Alternatively, you can backup decrypted versions of your save files using a tool like JKSV, and you can restore those saves on any Switch under any user using JKSV.
If your sysMMC is clean, you should update your sysMMC using the official method from the system settings. If you want to play online using your sysMMC, it must be on the latest version.
If your emuMMC is dirty, you should update the emuMMC using Daybreak. If you update your dirty emuMMC using the official method from the system settings, you will get banned. Your emuMMC should be on a relatively new version for game compatibility. 12.1.0 is supported by Atmosphere, so there's no reason not to update to this version using Daybreak on your emuMMC.
If you are not playing online and don't plan to play online, there's really no reason to even use an emuMMC.