The main firmware will overwrite the 256M root filesystem. The eMMC flash will overwrite the 32GB storage. Neither of these will touch any SD card installed.

If you formatted the 27GB partition, then this is on the eMMC and you probably want to reflash it. As for missing items, the eMMC flash is probably missing the preloaded map data, but that can be easily downloaded and installed anyway (using Nokia Map Loader). It may also be missing the manual, but I don't know for sure. There certainly shouldn't be anything major/irreplaceable missing from the downloadable flash files.