I agree. I would much rather just keep it running and have faster boot times. But it is what it is. I just switch less often between sysnand and emunand.
Another thing you can try is the new AIO Updater app. It will download the fw and extract it for you. I'm not sure if it does any sort of crc checking but the fw comes from the archive.org link that's on the website most people download their fw from. It's at least something else to try. You still use ChoidujourNX to update, the AIO Updater app just
downloads and extracts the fw for you.
I updated my sysnand using the built in Nintendo menu (running ofw button, not genuine boot). And then I updated my emunand using ChoidujourNX. So all of this is possible. We just need to track down why is failing for you.
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