Well, yes. ReiNAND has had firm partition protection for a while now. So, updating will not overwrite your firms with a retail NF. However, it still relies on external firmware files. So, if Nintendo updates NATIVE_FIRM, the "native_firmware.bin" file may need to be updated before the new FW version can be booted by Rei-Six. As history has shown, this depends on if Nintendo updates the minor version, and whether they make the other apps like the home menu require this as the new minimum version required in order to run. That is why rxTools remained usable for so long without updates (until 11.2 came out IIRC). The home menu remained bootable with 9.6 for all that time. But Nintendo probably won't make that mistake again.
Luma has been able to avoid this problem because it has the ability to extract the firmware files straight from the CTRNAND partition. But that also requires it to reload itself with it's reboot patches. Until recently, this required a "path.txt" file unless you were using Luma as the main payload (which I never have). I'm sure Crimson would love to add this feature, but it's complicated, and it was far more important to add these other patches first.
It's not really that hard to extract a new NF though. I could easily create a GM9 script that extracts the current NF (actually, I already have that part written for me, thanks to d0k3), copies it to the "rei" folder, and decrypts it, assuming that would work. I have to admit, I'm not really sure how the current "native_firmware.bin" is generated. Though I'm guessing they're just using "copy/b" or "cat" to concatenate them together, and that the CFW sorts them out via a byte pattern search for the header or something.
