Yes, it backs up the unpatched files (technically it removes the patch from the file then backs that up).
All you have to do is run clean up, or run genuine boot, then shut the system down and remove the chip.
I decided to bank on that theory of yours, so I managed to resurrect my Switch with SXOS and its wires connected.
One of the issues I was having with SXOS 3.0.5BETA was that it no longer allowed my Switch LITE to go to sleep. I couldn't work around that and the fact it was just ONE of the issues, not to mention the memory card ones.. ugh
Anyway, I performed the cleanup. It successfully completed. Then I proceeded to disconnect the wires of the hacking board (although it's still soldered onto my system) and I can now finally boot my system without having to desperately hope for it to do so.
And speaking of that sleep-mode issue (SXOS would immediately shutdown my console, whether it came to sleep after some time of inactivity or when I pressed the POW button), I checked my sysnand's settings and it was still sitting on 10.0.1. So I figured updating the firmware could fix this, maybe? So I did the upgrade, system restarted successfully without my intervention and it got to the welcome area. Then I pressed the POW button, it went to sleep. Pressed it again and it came up. But it was short-lived. I tried it again, but this time it shutdown my device.
Now, whenever my system goes to sleep, it shuts down and I have to keep my finger pressed down on POW for 14 seconds. After that, I'm able to turn it on. My question is, is that because the board is still soldered on? Any way to fix it now that I'm back to OFW? I just want that thing gone from my system, its led still lights up a blue-ish white upon powering it on and be able to go to sleep and out of it again.
Side-quest: Would you take my Switch Lite and get the hacking board removed for me? I'll pay you for your services.