If you're on Windows, I think you can use that Nokia Software Update app you found. If you're on Linux (or like using the command line), then the "Updating Tablet Firmware" wiki page is right for you. Reflashing an N810 or N900 is pretty much exactly the same process; you just use a different firmware file. And yes, NITDroid does keeps the Maemo initial bootloader around and just replaces the kernel (AFAIR), initfs and rootfs. Now that I think about it, it's *possible* that the Nokia Software Update program might not correctly identify the device if it's running NITDroid, but flashing from the command line (on WIndows, Mac or Linux) should be no problem. And if you get stuck, just stop back here and ask.

-John