This is probably the wrong area to ask this, but I couldn't find a better place.

I'm a very paranoid person. Earlier I ran a DS firmware dump from my R4i Gold on my 3DS, and it asked to to calibrate screen, set up profile, etc.

It completely wiped out the DS/i profile section on my 3DS, but I went back in and restored it.

Something interesting I found is that, while configuring the firmware, even if I "set" the time incorrectly, it would be correct when moving onto the next step. Completely ignoring what I had entered and going with the 3DS' time/date anyway.

Which brings me to my main question: Does calibrating the touch screen through the DS firmware (or any DS ROM) actually re-calibrate the 3DS touch screen, or would it have also ignored that as well and be overridden by what it's already calibrated to?

 

That, and only some portions of NVRAM are fully accessible in DS Mode. You can read it all, but you can't write to certain sections of it. It's entirely possible that screen calibration, date, time and other such settings were designed to be set in 3DS Mode and since Nintendo couldn't possibly anticipate users running DS firmware on the thing, you were met with an error.