That sounds counter-intuitive to say the least. #1 rule of any exploited console is to never update. Yeah, I prefer to keep sysNAND original firmware too.The way they handle update is by updating your sysNAND to the latest, followed by dumping your sysNAND's firmware and installing it via Daybreak on emuNAND. I usually download firmware files from that certain site we aren't allowed to link to and just update via Daybreak, leaving my sysNAND on whatever firmware it was previously on. I'll keep it on lowest possible, just in case another exploit is found that works on firmware I'm at.
I updated it once. Maybe 2-3 years ago. Seems to work fine. I think it's a knock off from Aliexpress.As for the dongles, if you have a knock-off, you probably have a somewhat recent version of Hekate's payload which doesn't need to be updated as it checks whether bootloader/update.bin exists on your SD card and, if newer, launches that one. Otherwise, if it's official and if you're using Atmosphere's fusee.bin, you'll need to update that one for it to work.
I wouldn't know how to delete sys-patch now. I'll let it be, though it seem the reason why I had troubles is because I did have some clutter on atmosphere/content folder.While sigpatches should be enough for game backups to work, you can install sys-patch module as well. Having both sigpatches and sys-patch at the same time should cause no conflict at all, but it's recommended to stick to one that works for you in order to reduce the clutter on your SD card since they are doing the same thing.
I'm always scared to update the Switch because it's so compicated. Though I just learned that new version of DBI can install games directly from SD card which is a very good development. Establishing connection with PC is a major headache.